IMGT/3Dstructure-DB and IMGT/2Dstructure-DB Documentation

IMGT®, the international ImMunoGeneTics information system®

Introduction

IMGT/3Dstructure-DB [1] is part of IMGT®, the international ImMunoGeneTics information system®, the high-quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates species, immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI), created in 1989 by Marie-Paule Lefranc (Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Université Montpellier II and CNRS) and on the Web since July 1995. IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

In 2008, amino acid sequences from INN/WHO were entered in IMGT/2Dstructure-DB, a section of IMGT/3Dstructure-DB. They comprise those of monoclonal antibodies (IG, mAb) and fusion proteins for immune applications (FPIA).

In 2010, amino acid sequences from Kabat were entered in IMGT/2Dstructure-DB. They comprise those of immunoglobulin superfamily sequences collected and manually culled from the scientific literature, especially the book "Sequences of proteins of immunological interest, Vol.I and II", U.S. Department of Health and Human Services, National Institute of Health.

IMGT/3Dstructure-DB provides a unique expertised resource on IG, TR, MH and RPI with known 3D structures. Structural data are extracted from the Protein Data Bank PDB. The IMGT/3Dstructure-DB standardized information includes IMGT annotation on the sequences, 2D structures (IMGT Colliers de Perles) and 3D structures of IG, TR, MH, and RPI with known 3D structures which are available in IMGT/3Dstructure-DB cards [2-7].
Annotations are according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts [8-10].
Three-dimensional structure analysis includes chain details and contact analysis at different levels (domain internal stability, domain/chain interface, residue) that are particularly relevant for immunological proteins like IG, TR and MH, as they interact specifically with a great number of molecules.

Domain sequences are renumbered according to the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN [11], to the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN [12], and/or to the IMGT unique numbering for G-DOMAIN and G-LIKE-DOMAIN [13]. Each IMGT/3Dstructure-DB card is associated to a coordinate flat file with IMGT renumbered residues.

Screenshots are in blue rectangles and data processing details are in green rectangles.

The screen captures have been updated, please note the text has not yet been updated.

IMGT/3Dstructure-DB Query page

The IMGT/3Dstructure-DB Query page shows, at the top of the page, the status of the database (Current date, the total number of entries and its decomposition (PDB, INN) and the date of the last update) and at the bottom of the page, the last entries and the access to the IMGT tools (IMGT/DomainDisplay, IMGT/Collier-de-Perles, IMGT/DomainGapAlign, IMGT/DomainSuperimpose and IMGT/mAb-DB).

The IMGT/3Dstructure-DB Query page allows six types of search, the possibility to align user's sequences against whole IMGT/3Dstructure-DB entries using FASTA and offers visualization choice for the results.

IMGT/3Dstructure-DB six types of search

Search by PDB or INN code or Molecule Name (receptor or ligand)

• Entry code (PDB, INN, PROTEIN)

  The IMGT/3Dstructure-DB entry code (ID) is identical to the PDB code, INN code or PROTEIN code. PDB code is an alphanumeric code (Ex : 1ao7), INN code is a numeric code (Ex: 7637) while PROTEIN code is an alphanumeric code which lenght is equals to 6 (Ex : p00054).

  An AutoComplete behavior is available for this field. AutoComplete works in the following manner: as you type in the beginning of a PDB code previous entries are pulled from a storage area and you may elect to simply select one of these entries. By selecting an entry, you no longer have to input the string because AutoComplete finishes entering the string for you.

• IMGT molecule name

  IG, TR, MH or RPI protein name and, if present, ligand. An IMGT molecule name is either a name retrieved from the literature or a name modified by IMGT® or a name added by IMGT®. The search by IMGT molecule name is case insensitive.

  The query "%>%" will retrieve all protein mutants for which the amino acid change(s) are indicated with the signe '>' in the IMGT molecule name.

  IMGT molecule naming rules

  IG and TR: When the molecule name is undefined in the PDB file, an IMGT standardized name is created which comprises letter(s) and number(s) for the fragment type and the chain type, and if necessary, a hyphen followed by a number (ex: CH2E-1, FcE-1, FcE-2, FcG1-1, FcG1-2, FcG1-3, Fv-1, FabM).w

  Mutants: IMGT standardized names for the protein mutants (ex: mutants of Len and Rei) comprise amino acids changes described according to the IMGT description of mutations (IMGT Scientific chart).

  Particularities in protein designations: The designation 'Newm' is used, in IMGT/3Dstructure-DB (ID: 7fab) for the human IgG1 myeloma protein Fab (designated as 'New' in PDB). This IMGT® designation Newm avoids confusion with the human 'New' Bence Jones Protein, that has been sequenced before 'Newm' (Particularities in protein designations: Human immunoglobulins: New and Newm).

Search by IMGT entry type using IMGT-ONTOLOGY concepts

This section allows users to search entries using the IMGT-ONTOLOGY concepts (IDENTIFICATION, DESCRIPTION, CLASSIFICATION and NUMEROTATION) for each type of IMGT entry. This kind of search uses linked select elements. Linked select elements are two or more selects, where choosing a value in one changes the available values in some of the rest. For example, selecting an IMGT receptor type will updates the 'IMGT receptor description' select to only contain receptor description from the IMGT receptor type selected. In the same way, selecting an IMGT group will updates the 'IMGT subgroup' select to only contain subgroup(s) from the IMGT group selected.

Choose an IMGT entry type and then a: Species (also includes Camelized, Chimeric, Humanized, Caninized and Synthetic), IMGT receptor type (IG, TR, MH, RPI, FPIA or Any), IMGT receptor description, IMGT chain description, IMGT group, IMGT subgroup, IMGT gene or IMGT allele.

Options menus allows you to refine your research (MH1 and MH2 for IMGT receptor type; FV, SCFV, FAB, FC and RPI-MH1Like for IMGT receptor description).

Search by Position

The form allows an easy search by the following criteria:

• Residue@Position, that is presence of a given amino acid at a given position. Position is according to the IMGT unique numbering
• Local Structure@Position, with the following criteria:
  • Secondary structure (alpha helix, 3-10 helix, PI-helix, extended conformation, isolated bridge, turn or coil)
  • Phi and Psi angles (in degrees)
  • Accessible surface area (ASA) in angstrom² (Ų)
• Atom contact type between two positions

Search using a complex query

A complex query can be performed. It is made up of a list of structural criteria coordinated by parentheses and boolean operator (AND and OR).
The query can be entered in the text area, either manually, or with the Javascript helper tool (available below the text area). The selection of a structural criteria in the scrolling list of the helper tool will show the corresponding fields to be filled in. A 'Quick Help' is available for each criterion.
The different criteria currently implemented are:

• Contact: Atom contact type between two positions. Example: 'contact(111V,108V,HB)>0' will query for IMGT/3Dstructure-DB entries which contain an hydrogen bond between position 111 and 108 in a V type domain (111V,108V)
• HB: Hydrogen bond between two amino acids (STRIDE hydrogen bonds). Example: 'HB(111V,108V)' will query for IMGT/3Dstructure-DB entries which contain an hydrogen bond between position 111 and 108 in a V type domain (111V,108V) as determined using the algorithm STRIDE
• SS: Secondary structure of a given residue. Example: 'SS(112V)=H' will query for IMGT/3Dstructure-DB entries which contain at position 112 in a V type domain (112V) a residue in the phi/psi helix conformation
• Phi and Psi: Amino acid φ and ψ angles in degrees
• ASA: Accessible surface area (in square angstroms, Ų)
• AA: Amino acid type is in the one letter abbreviation. Example: 'aa(89V)=M' will query for IMGT/3Dstructure-DB entries which contain at position 89 in a V type domain (89V) a methionine (=M)
• Length and Pattern: CDR-IMGT length (only available for the V type domain)
• Pattern: Amino acid pattern in a CDR-IMGT. As an example '[GSE]..L..Y' will query for IMGT/3Dstructure-DB entries which contain sequences with a CDR-IMGT pattern starting with an G,S or E, the fourth amino acid being a leucine and the seventh amino acid being a tyrosine
• Description: IMGT domain description
• Species: Species here includes humanized, camelized, chimeric and synthetic
• Group: Structure's gene group
• Gene: Wanted gene name

Example of combined query
group=TRAV AND length(CDR3)=13	Will query for IMGT/3Dstructure-DB entries which contain domain sequences from the TRAV group and a CDR3-IMGT of 13 amino acids.
length(CDR1)=8 AND aa(29V)=V	Will query IMGT/3Dstructure-DB entries which contain domain sequences with a CDR1-IMGT of 8 amino acids AND with, at position 29 of the V type domain (29V), a valine (=V).

Search by Resolution, Release date, Experimental method or bibliographical references

• Search by Resolution, Release date, Experimental method
• Resolution. Six value ranges are available: 0 - 1.00 Å, 1.01 - 2.00 Å, 2.01 - 3.00 Å, 3.01 - 4.00 Å, 4.01 - 5.00 Å and 5.01 - 6.00 Å.
• Release date. Choose the year of the PDB's release.
• Experimental method. Choose among 9 experimental methods: Electron microscopy, NMR, NMR, 18 structures, NMR, 20 structures, solution scattering, solution scattering, theoretical model, theoretical model, X-ray diffraction or X-ray diffraction, single crystal.
• Search by References
• First choose the type of reference (PDB or PubMed)
• After, select Author, Journal, PMID (for PubMed references) and Year
This kind of search uses linked select elements. For example, selecting an author will updates the 'Journal' select to only contain Journal(s) from the author selected.

IMGT/3Dstructure-DB visualization choice for the results

At the top of the IMGT/3Dstructure-DB Query page, the user can choose to view the results as "Overview" or "Domain and sequence alignment". These two choices will display a list of IMGT/3Dstructure-DB entries or a list of chains respectively. .

The Overview offers many choices:

• IMGT allele(s) name
• PDB references information are extracted from the coordinate file
• PubMed references information is from NCBI
• IMGT complex name

An additional choice, "Reference view" is available at the bottom of the IMGT/3Dstructure-DB Reference query page.

FASTA chain alignment

Users can FASTA their own sequences against the IMGT/3Dstructure-DB sequences using the 'Search using alignments' tool. Users can choose the numbers of results to display

IMGT/3Dstructure-DB Results

The result presentation depends on the visualization choice made at the IMGT/3Dstructure-DB Query page. On top of each result page, the visualization choice and the query are recalled, and the number of results is shown. For results which correspond to a list of chains (and not to a list of entries) it is recalled, between parentheses, that the number of results correspond to the 'number of chains containing the selected domain or region'. An additional result presentation corresponds to 'References'. The list of results is sorted by ID (entry or chain).

Overview

The 'Overview' results provide a list of Entries.

The Overview results page displays IMGT/3Dstructure-DB entries that satisfy the query, with for each entry the following information:

• IMGT entry ID. Clicking on the entry ID gives access to the IMGT/3Dstructure-DB card.
• IMGT molecule name. (see IMGT molecule naming rules)
• IMGT receptor type or IMGT receptor description or IMGT chain description. (see IMGT receptor and chain description rules)
• Species. The chain species (includes Camelized, Chimeric, Humanized and Synthetic. It may therefore be different from gene species, for example a chimeric chain may have Homo sapiens and Mus musculus genes).
• Ligand(s). Include ligands and, by extension, proteins other than IG, TR, MH or RPI.
• Experimental technique. X-ray diffraction, NMR, theoretical model.
• Resolution. Resolution of X-ray diffraction in angstrom (Å).
• PDB release date. Release date in the Protein Data Bank.

Domain type sequences

The 'Domain type sequences' results provide a list of chains containing the selected domain type.

The 'Domain and sequence alignment' result page displays a list of IMGT/3Dstructure-DB chains with, for each chain:

• chain ID. Clicking on the chain ID gives access to the corresponding IMGT/3Dstructure-DB card.
• Species
• IMGT molecule name
• IMGT domain description
• FR-IMGT lengths
• CDR-IMGT lengths
• Amino acid sequences. Sequences of the domain type, with gaps and amino acid positions according to the IMGT unique numbering.

Reference view

'Reference view' is only available from the IMGT/3Dstructure-DB Reference query page.
It displays the following fields for bibliographical references extracted from the coordinate file: IMGT entry ID, Authors (PDB), Title (PDB), Year (PDB), Authors (PubMed), Title (PubMed) and Year (PubMed).
Clicking on the IMGT entry ID gives access to the IMGT/3Dstructure-DB card.

IMGT/3Dstructure-DB card

The 'IMGT/3Dstructure-DB card' is the core unit of IMGT/3Dstructure-DB. Indeed, there is one card per IMGT/3Dstructure-DB entry and this card provides access to all data related to that entry.

IMGT/3Dstructure-DB card header

The IMGT/3Dstructure-DB card header contains:

For PDB entries, a summary table with:

• IMGT molecule name: IG, TR, MH or RPI IMGT protein name (see IMGT molecule naming rules)
• Receptor type: IG, TR, MH or RPI.
• IMGT receptor description: IG, TR, MH or RPI IMGT receptor description (see IMGT receptor description rules) and, for other molecules: Amino acid, Carbohydrate, Chemical compound, DNA, Ion, Peptide, Protein or RNA.
• Ligand(s): Ligand or protein name (protein other than IG, TR, MH or RPI).
• Species: Species (including Camelized, Chimeric, Humanized and Synthetic). Latin names are written in italic.
• Crystallographic complex (CC): Proteins are identified as belonging to the same crystallographic complex (CC) when two of their chains have at least 15 amino acid contacts or if one of the chains in contact is less than 20 residue long.
  A manual expertise is also sometimes required.
• IMGT chain ID: A chain identifiant comprises the ID code, an underscore and the chain letter.

For INN entries, a summary table with:

• IMGT molecule name: IG, TR, MH or RPI IMGT protein name (see IMGT molecule naming rules)
• Receptor type: IG, TR, MH or RPI.
• IMGT receptor description : IG, TR, MH or RPI IMGT receptor description (see IMGT receptor description rules) and, for other molecules: Amino acid, Carbohydrate, Chemical compound, DNA, Ion, Peptide, Protein or RNA.
• Specificity
• Species: Species (including Camelized, Chimeric, Humanized and Synthetic). Latin names are written in italic.
• IMGT chain ID: A chain identifiant comprises the ID code, an underscore and the chain letter.

Below the summary table are added:

• Experimental technique : X-ray diffraction, NMR, theoretical model
• Resolution : X-ray resolution in angstrom
• PDB Release date : Release date in the PDB
• IMGT complex name

Seven or eight (if Paratope and epitope are present) tabs give access to:

• Tabs for PDB entries:
• Tabs for INN entries:

• Chain details
• Contact analysis. Access to the IMGT/3Dstructure-DB Domain contacts (overview) for this coordinate file. Only available for PDB entries.
• Paratope and epitope
• 3D Visualization (JSmol). Only available for PDB entries.
• Renumbered IMGT file. Access to the renumbered coordinate file according to the IMGT unique numbering. The "download" link directly downloads the renumbered IMGT file (in gzip format).
• INN definitions and properties. Contains English, French and Spanish definitions, physico-chemical properties, Proposed and Recommended lists. Only available for INN entries.
• IMGT numbering comparison. Comparison of the residue numbering in the IMGT file and the PDB file.
• Reference and links
• Printable card

The Results from 'Paratope and epitope', 'Chain details' and 'Contact analysis' are detailed in the next sections.

Chain details

The 'Chain details' comprise information first on the chain itself, then per domain. The 'Chain details' section also gives information on associated ions and/or molecules that include ions, water and chemical molecules other than proteins or nucleic acids.

• Chain ID: Note that chain identifiant can be different in IMGT file compared to PDB file to correct misassignment.
• Chain length:
• IMGT chain description: Chains are described with standardized IMGT labels (listed in IMGT standardized keywords and labels for IG, TR and MH for proteins and 3D structures). The different domains and their position in the chain are also represented.
• Chain sequence: The chain sequence is an amino acid sequence created by comparing the sequence of the primary sequence section (SEQREF) and of the atom coordinate section (ATOM) of the PDB file. A mask is also created, to inform if the residue is present, or not, or different in the sequence of the atom coordinate section.
  • Residues not present in the atom coordinate section (ATOM) are writen in italic.
  • Residues other than amino acids are indicated with their three code letters enclosed in parentheses.
  • Amino acid differences with the closest IMGT allele sequence, shown in orange (these amino acid changes are identified by the IMGT/DomainGapAlign tool, integrated in IMGT/3Dstructure-DB and IMGT/2Dstructure-DB).
  The IMGT region delimitations are indicated over the sequence. The domain number in the chain, shown by the letter D followed by a number between square brackets, for example [D1] for the first domain. Colors for the visualization of regions and domains, for examples:
  • green for the V-REGION, red for the (N-D)-REGION and orange for the J-REGION of the IG and TR V-DOMAIN,
  • yellow color for the L-REGION,
  • blue color for the regions (e.g., HINGE-REGION) and domains (e.g., C-KAPPA, C-LAMBDA, CH1, CH2, CH3) of the IG and TR C-REGION.
  This is according to Color menu for regions and domains.

  Identification of the '(N-D)-REGION' region

  The '(N-D)-REGION' is arbitraly delimited by the lengths of the untrimmed germline V-REGION and J-REGION. If nucleotide sequences are available, it is recommended to use IMGT/V-QUEST for an accurate delimitation and analysis of the junction.

  If javascript is enabled on your browser, every residue (except those in italic) is clickable and gives access to its IMGT Residue@Position card.

  The links Sequence in FASTA format and Sequence in IMGT format are for

• Contact sites (pMH only): IMGT pMH contact sites provide IMGT Collier de Perles for G-DOMAIN with identification of the eleven IMGT contact sites for the standardized analysis of the peptide/MH contacts 7.

Domain description of a chain

The different domains which are parts of a chain, are described in details in a similar format. They include:

• V-DOMAIN for IG and TR
• V-LIKE-DOMAIN for proteins other than IG or TR
• C-DOMAIN for IG and TR
• C-LIKE-DOMAIN for proteins other than IG or TR
• G-DOMAIN for MH
• G-LIKE-DOMAIN for proteins other than MH

The display includes, for each domain:

• IMGT domain description: Domains are described with standardized IMGT labels (listed in IMGT standardized keywords and labels for IG, TR and MH for proteins and 3D structures).
• IMGT gene and allele name: The 'Alignment details' link allows to view the results of the allele identification alignments. Eventually a 'Others' link appeared to show alleles that give the same alignment score for this domain, but a different score for the other domains (see above Gene and Allele).

  Notion of consensus between alleles

  Consistency between alleles regions of the same chain is taken into account through the field consensus. Indeed several alleles may correspond to the same region but some of these alleles may not be consistent with the alleles in other regions. For example, alleles identified for different DOMAINs of a REGION must be identical.

• 2D representation: 2D representation (Provides a link to 'IMGT Colliers de Perles' for V and C type domains, to IMGT Colliers de Perles on 2 layers, see 3.2.4 IMGT Colliers de Perles).
• Contact analysis: Contact analysis provides a link to Domain contacts (overview).
• CDR-IMGT lengths: CDR-IMGT lengths (only for V-DOMAIN and V-LIKE-DOMAIN) are given between brackets.
• Sheet composition: Beta strands of the two sheets (only for V and C type domains) are given between brackets.
• Domain amino acid sequence: Gaps and amino acid positions are according to the IMGT unique numbering. The IMGT CDR1-IMGT, CDR2-IMGT and CDR3-IMGT delimitations are shown for V type (V-DOMAIN and V-LIKE-DOMAIN) domains. If javascript is enabled on your browser, every residue is clickable (except those in italic) and gives access to its IMGT Residue@Position card.
• IMGT/DomainGapAlign results: A link to the IMGT/DomainGapAlign results is provided per domain. The results of IMGT/DomainGapAlign are identical to those displayed in the IMGT/2Dstructure-DB or IMGT/3Dstructure-DB card (with the indicated species, for example humanized sequences are run against Homo sapiens (human) V gene). It is possible to obtain IMGT/DomainGapAlign results, by comparison to a different species or to 'Any species'. In the Standard parameters and sequences section at the top of the page, click a selection in the Species list (for example, 'any' for 'Any species'), and then click on 'Align and IMGT-gap my sequences'.

IMGT Colliers de Perles

IMGT Colliers de Perles are 2D graphical representation of the domains based on the IMGT unique numbering.

IMGT Colliers de Perles are provided for V, C and G type domains. For the V and C type domains, they represent the immunoglobulin fold topology. Loops anchors are shown in square, highly conserved amino acids at a position are in red and hydrophobic positions found as hydrophobic in more than 80% such domain sequences are in blue. For the V type domains the CDR-IMGT lengths are written at the top of the page between brackets and they are colored according to the IMGT Scientific chart. In IMGT Colliers de Perles on 2 layers, hydrogen bonds are shown on the front layer, back layer and between the 2 layers.

Clicking on the residue in the IMGT Colliers de Perles gives access to The "IMGT/3Dstructure-DB Residue@Position" card.

IMGT Collier de Perles on one layer (chain 1bql_H V-DOMAIN)	IMGT Collier de Perles on two layers (chain 1bql_H V-DOMAIN)
IMGT Collier de Perles of MH class I (chain 1a1m_A)	IMGT Collier de Perles of MH class II (chain 1a6a_A II-ALPHA and 1a6a_B II-BETA)

Molecules other than proteins

Associated ions and/or molecules

• Code: Three or two letters code.
• Nb: Number of ions or molecules associated to the chains.
• Name: Name of the ion or molecule, from the PDB Chemical Component Dictionary.
• Formula: Formula of the ion or molecule, from the PDB Chemical Component Dictionary.
• IMGT/3Dstructure-DB Residue@Position card: If Javascript is enabled on your browser, clicking on the right column gives access to the IMGT Residue@Position card ions and/or molecules. If the number of residues exceed 4, 'Not shown' appears in this column.

Note that ions and/or molecules are individualized in IMGT when they are included by error in the PDB chain definition.

Contact analysis

IMGT pMH contact sites

IMGT pMH contact sites provide IMGT Collier de Perles for G-DOMAIN with identification of the eleven IMGT contact sites for the standardized analysis of the peptide/MH contacts 7.
The user can also download the table. The download contains two files. The first one provided chains details on a text file and the second one is the contact table on csv format.

IMGT/3Dstructure-DB Domain pair contacts (overview)

The IMGT/3Dstructure-DB Domain contacts (overview) analysis provides information on the contacts between domain and/or chain and on the internal contacts in an IMGT/3Dstructure-DB entry.

The domain/chain partners considered are designated as 'Set 1' and 'Set 2'. The number of residue contacts, the number of residues involved (total and per partner 1 and 2) and the number of atom contact types are provided.

Clicking on "DomPair" gives access to the 'IMGT/3Dstructure-DB Domain pair contacts of the selected pair of partners.

IMGT/3Dstructure-DB Domain pair contacts

IMGT/3Dstructure-DB Domain pair contacts provides information on the contacts between a pair of partners (indicated at the top of the page). Clicking on R@P gives access to the IMGT Residue@Position card (4.2.1 section).

For TR/pMH complexes, IMGT pMH contact sites are available in IMGT/3Dstructure-DB Domain pair contacts.

IMGT Residue@Position card

If Javascript is enabled on your browser the IMGT Residue@Position card is accessible by clicking on a residue either in the amino acid sequence or in the IMGT Collier de Perles.

A Residue@Position is a residue at an IMGT position, according to the IMGT unique numbering.

A Residue@Position is defined by:

• the position numbering (for example 23) according to the IMGT unique numbering
• the residue name in the 3-letter abbreviation and, between parentheses, in the one-letter abbreviation for amino acids (for example CYS (C))
• the IMGT domain description (for example V-KAPPA)
• the IMGT chain ID (for example 12e8_M)

An IMGT Residue@Position card provides structural information and contacts for a given Residue@Position:

• General information comprises the PDB file numbering, the IMGT file numbering, the residue full name and formula.
• Residue IMGT LocalStructure@Position comprises secondary structure, Phi and Psi angles and accessible surface area (ASA in square angstrom) given by the STRIDE program.
• Pair contacts provides the atom contacts number, type and atom contact categories for this residue with others. Clicking on the IMGT numbering gives access to the Residue@Position cards of these residues.

Paratope and epitope details

Epitope

Epitope description of IG/antigene, TR/peptide and TR/MH are provided. The MH/peptide interface is also provided in this section.

• Ligand name
• IMGT chain ID
• Epitope type: Discontinuous or linear.
• Residues: Residues which belong to the epitope order as in the AA sequence and without taking into accout spatial positions.
• With positions: Identify the positions with chain and IMGT unique numbering of the residues implicated in the interface/epitope.

IMGT paratope and epitope representations are also provided and display the amino acids implicated in pMH and TR/pMH complexes. The amino acids are shown as tables and in IMGT Colliers de Perles.

IMGT paratope and epitope of TR V-ALPHA/MH

IMGT paratope and epitope of TR V-BETA/MH

peptide/MH Interface

peptide/TR Interface

3D visualization with JSmol

The whole chain sequences are displayed in a box, indicating the chain ID, the IMGT Receptor description and the length of the chain. Users just have to click on a residue in sequences to visualize it in the JSmol (wireframe by default).

Users can view structures/molecules using a JSmol. The interface is composed of 5 sub-menus: Selection, View, coloration, IMGT and Paratope/epitope.

The Selection menu offers a selection by:

• predefined ensemble (All structure, Backbone, Sidechain or Water)
• IMGT receptor type (for example TR)
• chain ID (for example 1AO7H)
• IMGT domain description (for example V-KAPPA)
• CDR type (for example CDR1 V-ALPHA)

Receptor type, Chain ID, Domain description and CDR type are linked select elements. Linked select elements are two or more selects, where choosing a value in one changes the available values in some of the rest.
For example, selecting an IMGT receptor type will updates the 'Chain ID' select to only contain Chain ID from the IMGT receptor type selected.
In the same way, selecting a Chain ID will updates the 'IMGT domain description' select to only contain domain descriptions from the Chain ID selected.

The View menu offers a display in the:

• wireframe view
• spacefill view
• dots view
• ribbons view
• cartoon view
• trace structure view
• meshribbon view
• rocket view

The Coloration menu offers a display:

• using amino acid type color
• cpk colors
• chain colors
• charge colors
• structure colors
• green color
• red color
• yellow color
• blue color

The IMGT menu offers different displays, depending on the type and the receptor description of the structure, and using IMGT concepts:

• CDR-IMGT labels
• CDR-IMGT only (side view)
• Domain description
• Complex colored by chains and CDRs
• CDR-Ag contacts
• IMGT pMH contacts sites
• Paratope/epitope contact atoms
• TR/pMH contacts

The Paratope/epitope menu offers visualization of the different amino acids implicated in the choosen complex.

Renumbered file

Allows to view (or download) an IMGT coordinate file renumbered according to the IMGT unique numbering.
In the IMGT coordinate file the 'REMARK 410' lines which have been added provide IMGT specific information (IMGT molecule name, IMGT receptor description and chain codes), domain positions (with CDR-IMGT length for V type domains) and regions position and allele identification.

For Windows users, the gziped renumbered coordinate file is automatically unziped by the system. You just have to remove the .gz extension.

References and links

• Reference(s) from PDB
• Reference(s) from PubMed
• Related IMGT/3Dstructure-DB cards: Links to other IMGT/3Dstructure-DB entries which have a PDB bibliographical reference in common.
• External Links: Links to other structural databases for this coordinate file.

IMGT/3Dstructure-DB upgrade and new versions

Since version 4.3.0, the upgrade and new versions of IMGT/3Dstructure-DB and tools are indicated in the two files:

• Program versions
• Database releases

• 12nd of April 2010 (Version 4.2.0)

  IMGT/3Dstructure-DB contains 2246 entries (1820 PDB, 81 INN and 345 Kabat).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Addition of sequences from Kabat.
    • Amino acid sequences from Kabat were entered in IMGT/2Dstructure-DB. They comprise those of immunoglobulin superfamily sequences collected and manually culled from the scientific literature, especially the book "Sequences of proteins of immunological interest, Vol.I and II", U.S. Department of Health and Human Services, National Institute of Health.
  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus, Oncorhynchus mykiss, Rainbow trout and Rattus norvegicus) and from IMGT/HLA-DB database.

• 8th of March 2010 (Version 4.1.0)

  IMGT/3Dstructure-DB contains 1881 entries (1800 PDB and 81 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of Web interfaces for IMGT/3Dstructure-DB database.
    • Improvement of IMGT chain description, Chain sequence and IMGT domain description in the IMGT/3Dstructure-DB card, 'Chain details' tab:
      • Chain or domain description (Ex: TR-ALPHA = V-ALPHA + C-ALPHA)
      • Start and end positions of domains in the chain (Ex: TR-ALPHA = V-ALPHA (1-110) + C-ALPHA (112-115))
      • Number of the domains in the chain (Ex: TR-ALPHA = V-ALPHA (1-110) [D1] + C-ALPHA (112-115) [D2])
  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus, Oncorhynchus mykiss, Rainbow trout and Rattus norvegicus) and from IMGT/HLA-DB database.
  • Update of IMGT/DomainGapAlign tool.
    • Improvement of the Web interface and the display of results.
    • Highlight of the amino acids changes between the closest germline V-REGION (for 'V'), C-DOMAIN (for 'C') or G-REGION (for 'G') and the sequences submitted by users.
    • Results summary (corresponding to the closest genes and alleles) with:
      • for V-REGION: CDR-IMGT lengths, Number of different AA in CDR-IMGT (CDR3 not included), FR-IMGT lengths, Number of different AA in FR-IMGT, Number and list of AA changes.
      • for C-DOMAIN: Number of different AA in strands, turns and loops; Number and list of AA changes.
      • for G-REGION: Number of different AA in strands, turns and loops; Number and list of AA changes.
    • IMGT Colliers de Perles on one layer and IMGT Colliers de Perles on two layers (with and without AA changes).

• 10th of February 2010 (Version 4.0.2)

  IMGT/3Dstructure-DB contains 1855 entries (1775 PDB and 80 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Mus musculus, Oryctolagus cuniculus, Oncorhyncus mykiss and Danio rerio) and from IMGT/HLA-DB database.

• 29th of January 2010 (Version 4.0.1)

  IMGT/3Dstructure-DB contains 1835 entries (1765 PDB and 70 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus and Rattus norvegicus) and from IMGT/HLA-DB database.

• 1st of November 2009 (Version 4.0.0)

  IMGT/3Dstructure-DB contains 1753 entries (1698 PDB and 65 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of Web interfaces for IMGT/3Dstructure-DB database and IMGT/DomainDisplay, IMGT/DomainGapAlign, IMGT/Collier-de-Perles and IMGT/StructuralQuery tools.
    • Improvements of the web interfaces (5 types of search, linked lists, ...)
    • Improvement of Sequence in IMGT format in the IMGT/3Dstructure-DB card, section 'Chain sequence':
      • Plain (FASTA format)
      • With regions and domains
      • With FR-IMGT and CDR-IMGT
      • With cysteins involved in disulfide bridges and with N-glycosylation sites (INN)
      • With N-glycosylation sites (PDB)
  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database. Addition of 163 Rattus norvegicus IGKV genes and alleles (136 functional, 6 ORF and 21 pseudogenes).
  • Update of IMGT/DomainGapAlign tool.
    • Improvement of the Web interface and the display of results.
    • Highlight of the amino acids changes between the closest germline V-REGION (for 'V') or C-DOMAIN (for 'C) and the sequences submitted by users.
    • IMGT mutation and AA change description (see IMGT amino acid classes)
    • Results summary (corresponding to the closest genes and alleles) with: CDR-IMGT lengths, Number of different AA in CDR-IMGT (CDR3 not included), FR-IMGT lengths, Number of different AA in FR-IMGT, Number of AA class changes and List of AA class changes.
  • Update of 3D visualization with Jmol.
    • The whole chain sequences are displayed in a box, indicating th chain ID, the IMGT Receptor description and the lenght of the chain. Users just have to click on a residue in sequences to visualize it in the Jmol applet (wireframe by default)
    • The interface is now composed of 5 sub-menus: Selection, View, coloration, IMGT and Paratope/epitope.
    • Please go to 3D visualization with Jmol for more details.

• 29th of April 2009 (Version 3.1.0)

  IMGT/3Dstructure-DB contains 1655 entries (1616 PDB and 39 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Canis lupus familiaris).
  • Update of IMGT/2Dstructure-DB cards.
    • New tab for IMGT/2Dstructure-DB entries (INN): INN definitions. This tab contains informations about CAS number, Molecular formula, Glycosylation sites positions and Disulfide bridges positions.

• 25th of February 2009 (Version 3.0.0)

  IMGT/3Dstructure-DB contains 1609 entries (1570 PDB and 39 INN).

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Addition of amino acid sequences from INN/WHO.
    • Amino acid sequences from INN/WHO were entered in IMGT/2Dstructure-DB, a section of IMGT/3Dstructure-DB. They comprise those of monoclonal antibodies (IG, mAb) and fusion proteins for immune applications (FPIA).
  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus and Rattus norvegicus) and from IMGT/HLA-DB database.
  • IMGT/3Dstructure-DB cards visualization
    • Upgrade of Jmol (11.6.6 version).

• 20th of October 2008 (Version 2.1.4)

  IMGT/3Dstructure-DB contains 1487 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Rattus norvegicus and Oryctolagus cuniculus).
  • IMGT/3Dstructure-DB cards update
    • Addition of Sequence in IMGT format link in the IMGT/3Dstructure-DB card, section 'Chain sequence'.
    • Upgrade of Jmol (11.4.6 version).

• 13rd of June 2008 (Version 2.1.3)

  IMGT/3Dstructure-DB contains 1441 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus).

• 21st of March 2008 (Version 2.1.2)

  IMGT/3Dstructure-DB contains 1403 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Update of IMGT/DomainDisplay.
    • Update of the IMGT domain reference directory from the IMGT/GENE-DB database.
    • Improvement of the IMGT/DomainDisplay web interface.

• 6th of December 2007 (Version 2.1.1)

  IMGT/3Dstructure-DB contains 1303 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • IMGT/3Dstructure-DB card update
    • Visualization of Paratope and epitope in a separate tab.
    • Contacts available for all residues of Paratope(s) and epitope(s).

• 21st of August 2007 (Version 2.1.0)

  IMGT/3Dstructure-DB contains 1275 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • IMGT/3Dstructure-DB card update.
    • Addition of Sequence in FASTA format link in the IMGT/3Dstructure-DB card, section 'Chain sequence'.
  • Data update
    • MH1-ALPHA-LIKE receptor description in RPI receptor type (and not MH).
    • Renaming of CD1D gene: CD1D1 (Mus musculus), CD1D (Homo sapiens)
  • IMGT/DomainDisplay update
    • Default alignment of alleles * 01.
    • Fixed alignments (deletion of gaps) for MR1 and EPCR genes.
    • Deletion of H2-M4, M7-H2, H2-T10 H2-T24 and H2-PA genes.

• 15th of July 2007 (Version 2.0.5)

  IMGT/3Dstructure-DB contains 1269 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • IMGT/3Dstructure-DB Display results update.
    • New option available for display results: Gene(s) and Allele(s).

• 30th of April 2007 (Version 2.0.4)

  IMGT/3Dstructure-DB contains 1265 entries.

  IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:

  • Modification of the IMGT/3Dstructure-DB Query page.
    • Options available for search by receptor type (MH1, MH2) and by receptor description (FV, SCFV, FAB, FC and MH1-ALPHA-LIKE).
  • Modification of the IMGT/DomainDisplay Query page.
    • Options merged for the IMGT/DomainDisplay query page.
  • Modification of the IMGT/DomainGapAlign Query page and results.
    • IMGT/DomainGapAlign displays amino acid sequences with IMGT gaps and, for 'V', with delimitations of the FR-IMGT and CDR-IMGT, according to the IMGT unique numbering for V-REGION and V-DOMAIN, and for 'C', with delimitation of the strand and loops, according to the IMGT unique numbering for C-DOMAIN.
    • Clicking on the button "IMGT Collier de Perles" gives access to the IMGT Collier de Perles on one layer.

• 14th of February 2007 (Version 2.0.3)

  IMGT/3Dstructure-DB contains 1221 entries.

• 14th of January 2006 (Version 2.0.2)

  IMGT/3Dstructure-DB contains 1209 entries.

Acknowledgments

The first gene identification of the human IG proteins were carried out during a stay in the Laboratoire d'ImmunoGénétique Moléculaire, IGH, CNRS, Montpellier, France, by Dr. Gunilla Norhagen and Dr. Per-Erik Engstrom (May 1998) from the Huddinge University Hospital, Karolinska Institute, Huddinge, Sweden, Dr. Oksana Kravchuk (April-May 1999) from the Research Centre for Medical Genetics, Russian Academy of Medical Science, Moscow, Russia, and Dr. Olga Posukh (April-July 1999, July-October 2000) from the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia.

References

[1]	Kaas, Q., Lefranc, M.-P., IMGT/3Dstructure-DB and IMGT/StructuralQuery: a database and a tool for immunoglobulin, T cell receptor and MHC structural data, Nucleic Acid Res., 32:D208-D210 (2004). PMID:14681396.
[2]	Ehrenmann F., Kaas Q. and Lefranc M.-P., IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF, Nucleic Acid Res., 38:D301-D307 (2010). PMID:19900967.
[3]	Kaas, Q. and Lefranc, M.-P., IMGT/StructuralQuery: a tool for structural data analysis of immunoglobulin and T cell receptor variable domains, ECCB 2003
[4]	Kaas, Q. and Lefranc, M.-P., IMGT/3Dstructure-DB for immunoglobulin, T cell receptor and MHC structural data, ECCB 2002
[5]	Ruiz, M., Analyse bioinformatique standardisée IMGT des relations séquence-structure des immunoglobulines et des récepteurs T, Thèse de doctorat, Université Montpellier II, 2001
[6]	Kaas, Q., Analyse structurale des recepteurs d'antigenes dans IMGT et modelisation moleculaire, Thèse de doctorat, Université Montpellier II, 2005
[7]	Ruiz, M. and Lefranc, M.-P., IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures, Immunogenetics, 53:857-883 (2002). PMID:11862387.
[8]	Kaas, Q. and Lefranc M.-P., T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB, In Silico Biology, 5:0046 (2005).
[9]	Giudicelli, V. and Lefranc M.-P., Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 15:1047-1054 (1999).
[10]	Lefranc, M.-P. , Giudicelli, V., Ginestoux, C., Bosc, N., Folch, G., Guiraudou, D., Jabado-Michaloud, J., Magris, S., Scaviner, D., Thouvenin, V., Combres, K., Girod, D., Jeanjean, S., Protat, C., Yousfi-Monod, M., Duprat, E., Kaas, Q., Pommie, C., Chaume, D. and Lefranc G., IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biology, 4:17-29 (2004).
[11]	Lefranc, M.-P., Clement, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, I., Combres, K., Ginestoux, C., Giudicelli, V., Chaume, D. and Lefranc G., IMGT-Choreography for Immunogenetics and Immunoinformatics, In Silico Biology, 5:45-60 (2005).
[12]	Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains, Dev. Comp. Immunol., 27:55-77 (2003). PMID:12477501.
[13]	Lefranc, M.-P., Pommié, C., Kaas, Q., Duprat, E., Bosc, N., Guiraudou, D., Jean, C., Ruiz, M., Da Piedade, L., Rouard, M., Foulquier, E., Thouvenin, V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains, Dev. Comp. Immunol., 29:185-203 (2005). PMID:15572068.
[14]	Lefranc, M.-P., Duprat, E., Kaas, Q., Tranne, M., Thiriot, A. and Lefranc G., IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily MhcSF G-LIKE-DOMAIN, Dev. Comp. Immunol., 29:917-938 (2005). PMID:15936075.

Created:

01/10/2001

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB development:

IMGT/3Dstructure-DB was implemented by Manuel Ruiz (2001) and has been developed since 2001 by Quentin Kaas, since 2006 by François Ehrenmann and Zohra Ouaray and since 2011 by Caroline Tournier and Patrice Duroux

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB scientific officer:

Marie-Paule Lefranc

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