IMGT/3Dstructure-DB and IMGT/2Dstructure-DB Query page

Version 4.13.0 (2024-05-23)
- Fixed an issue in the processing of 'Search by structural query' which always gave an empty result and/or an incorrect syntax error.
Version 4.12.5 (2023-12-14)
- Recover the search based on 'Molecule name (receptor or ligand)' value
Version 4.12.4 (2022-06-03)
- Remove broken generated URL containing hash characters in sequence value
Version 4.12.3 (2019-11-17)
- Addressed an issue with the database server where some queries have empty column results
10th of October 2016 (Version 4.12.2)
- Remove small bugs introduced by the previous changes when querying the database
- Solve JavaScript hang when loading query page with Internel Explorer
26th of September 2016 (Version 4.12.1)
- Handle A domain type
- Add IMGT complex names field to structures and queries (show IMGT complex names on the overview, search a complex containing a specified character)
- Add field 'CPCA' on IMGT receptor type on the query page
- Add IMGT release date on structures when available
- Add new fields 'Epitope ID' and 'CHEBI ID' on 3D structure 'References and links' page, when available. Add the word 'Reference ID' to qualify the existing link
- Change 'External links' view, on 3D structure 'References and links page', to take into account structures with more than one MMDB reference
- Correct insertion bug on IMGT/Collier de Perles tool for F-DOMAIN
- References search request errors correction
- Update the documentation
- Update database schema
21th of April 2016 (Version 4.12.0)
- Change 'Paratope and epitope' view to show interfaces by couples
- Switch Jmol visualization from using Java Applet to using Javascript Applet
- Handle F domain type
- Other minor improvements
23th of September 2015 (Version 4.11.1)
- Ligand contacts are back in 'Contact analysis' view
- Highlight contacts to CDR-IMGT amino acid using color in Residue@Position as in domain pair contacts
19th of February 2015 (Version 4.11.0)
- Consideration of INN code with more than four digit
- Consideration of accented characters for INN french definition
- Add IMGT/mAb-DB card(s) and IMGT/3Dstructure-DB links to the 'References and links' rubric when existing
- Redefinition of HINGE-REGION in the chain sequence
- Change of domains' colors in the chain sequence
- Add download file for pMH contact sites
- Remove some chemical compounds and isolate carbohydrate from ligand components (they are now in the rubric "Associated ions or molecules" at the page's bottom)
9th of April 2014 (Version 4.10.0)
- Redesign query page that includes structural query elements (IMGT/StructuralQuery is gone)
- Change 'Domains and sequence alignment' output
- Better output for 'IMGT gene(s) and allele(s) name' display result
- Remove bug in 'Search using alignments' and switch external program from FASTA to GLSEARCH
- Improve Jmol visualization (CDR anchor, CDR zoom-in, themes)
- Add external links to Immune Epitope Database (IEDB) assay for corresponding entries
- Remove some Javascript bugs
- Many internal changes
25th of March 2013 (Version 4.9.0)
- IMGT/3Dstructure-DB contains 2802 entries (2290 PDB, 177 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with minor fixes:
  1. IMGT/DomainDisplay and IMGT/DomainGapAlign have now their own version line (see their documentation for current change)
  2. Improvement of IMGT/3DstructureDB cards.
    - Do not overwrite domain delimitations by region ones in the chain sequence ruler and use background color instead.
5th of March 2012 (Version 4.8.1)
- IMGT/3Dstructure-DB contains 2686 entries (2214 PDB, 137 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with minor fixes:
  1. IMGT/Collier-de-Perles
    - Remove too strong Javascript check for 'Numbering labels' field.
  2. Improvement of IMGT/3DstructureDB cards.
    - Better chain description with domain delimitations.
6th of October 2011 (Version 4.8.0)
- IMGT/3Dstructure-DB contains 2634 entries (2171 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/StructuralQuery
    - Modification of IMGT/StructuralQuery Query page, available at IMGT/StructuralQuery.
      The structural query is available for complexes (Paratope/epitope, Peptide/MH, Ligand category and Peptide length).
  2. IMGT/Collier-de-Perles for Scavenger domain (S domain)
    - Drawing of standardized IMGT 2D graphical representations of protein S domains is available at IMGT/Collier-de-Perles.
      See IMGT Collier de Perles for S domain.
  3. Improvement of IMGT/DomainDisplay and IMGT/DomainGapAlign.
    - Scavenger type domain (S type domain) is available in IMGT/DomainDisplay and IMGT/DomainGapAlign.
13th of September 2011 (Version 4.7.0)
- IMGT/3Dstructure-DB contains 2623 entries (2160 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/DomainDisplay.
    - Modification of table of polymorphisms results, available at IMGT/DomainDisplay.
      IMGT/DomainDisplay Allelic polymorphisms are now sorted out by IMGT receptor type, Species, IMGT group and IMGT domain type. IMGT domain label and domain number are available. An allele is identified by the mutations of its sequence compared to the reference sequence designated as *01. Polymorphic positions are indicated in red letters.
      See Table of polymorphisms documentation.
    - Moreover, table of polymorphisms now provides HINGE-REGION and J-REGION.
  2. IMGT/3Dstructure-DB cards (3D visualization).
    - Upgrade of Jmol (12.0.49 version).
11st of May 2011 (Version 4.6.0)
- IMGT/3Dstructure-DB contains 2513 entries (2064 PDB, 114 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/3Dstructure-DB Domain pair contacts
    - Addition of the visualization of IMGT pMH contact sites in IMGT/3Dstructure-DB Domain pair contacts for TR/pMH complexes (see as an example Contacts of G-ALPHA1 and Peptide)
  2. Improvement of "Paratope and epitope" section
    - Epitope/paratope representations: display of the amino acids implicated in pMH and TR/pMH complexes. The amino acids are shown as tables and in IMGT Colliers de Perles. See as an example the 1ao7 PDB (TR/pMH1 complex).
  3. IMGT/3Dstructure-DB cards (3D visualization).
    - Upgrade of Jmol (12.0.42 version).
  4. MHC replacement by MH
    - In IMGT/3Dstructure-DB and associated tools, major histocompatibility complex (MHC) has become major histocompatibility (MH), and MHC superfamily (MhcSF) has become MH superfamily (MhSF). These changes mainly concern the IMGT-ONTOLOGY concepts of DESCRIPTION, IDENTIFICATION and CLASSIFICATION.
4th of March 2011 (Version 4.5.0)
- IMGT/3Dstructure-DB contains 2457 entries (2010 PDB, 112 INN and 345 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/DomainDisplay.
    - Table of polymorphisms available.
      IMGT/DomainDisplay Allelic polymorphisms are queried through a web interface, using different sections (Species, IMGT receptor type, IMGT group, IMGT subgroup, IMGT gene and/or IMGT domain type. An allele is identified by the mutations of its sequence compared to the reference sequence designated as *01. Polymorphic positions are indicated in red letters.
      See Table of polymorphisms documentation.
  2. Improvement of IMGT/DomainGapAlign.
    - Results of IMGT/DomainGapAlign tool are now sorted by decreasing percentage of identity (decreasing Smith-Waterman score in previous versions).
  3. IMGT/3Dstructure-DB cards (3D visualization).
    - Upgrade of Jmol (12.0.34 version).
14th of September 2010 (Version 4.4.0)
- IMGT/3Dstructure-DB contains 2346 entries (1917 PDB, 94 INN and 345 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/DomainGapAlign.
    - Addition of a new parameter (Smith-Waterman score) for the display of aligments. The user can select the minimum or maximum Smith-Waterman score for the alignments to display (For example, choosing a "Smith-Waterman score above 200" will provide and display alignments whose Smith-Waterman score is superior to 200).
    - In the "Results summary" section, the AA changes are shown in FR- and CDR-IMGT, and now in strands and loops.
8th of July 2010 (Version 4.3.0)
- IMGT/3Dstructure-DB contains 2300 entries (1871 PDB, 94 INN and 345 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new functionalities:
  1. Improvement of IMGT/3Dstructure-DB Query page
    - Improvement of Search for complexes type of search:
      - Addition of Peptide length: search by Peptide length can retrieve structures which are in contacts with peptide(s) whose length is chosen in the drop-down list.
    - Improvement of Display results:
      - At the bottom of the IMGT/3Dstructure-DB Query page, the user can choose to view the results as "Overview", "Domain type sequences", "FR-IMGT and CDR-IMGT sequences" (only available for the V type domain)
      - These three choices will display a list of IMGT/3Dstructure-DB entries or a list of chains
      - Users can visualize all FR and CDR-IMGT sequences in one click
  2. Improvement of IMGT/DomainDisplay.
    - Highlighting of alleles polymorphisms: when several alleles are shown, the amino acid changes are indicated in red letters. These polymorphic mutations are reported in Tables of alleles. Currently, the amino acid changes are indicated for V and C type domains.

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

(2004).

[1]	Kaas, Q., Lefranc, M.-P. (2004) 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. PMID:14681396
[2]	Ehrenmann F., Kaas Q. and Lefranc M.-P. (2010) 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. 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., (2002) IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures. Immunogenetics, 53, 857-883. PMID:11862387,
[8]	Kaas, Q. and Lefranc M.-P. (2005) T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB. In Silico Biology 5:0046
[9]	Giudicelli, V. and Lefranc M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics 15:1047-1054
[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
[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 first 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

Contact: Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr

Editors: Quentin Kaas (2001-2007), François Ehrenmann (2006-2011), Caroline Tournier (2011-2013), Typhaine Paysan-Lafosse (2013-2016), Anjana Kushwaha (2017) and Patrice Duroux

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB program versions

IMGT®, the international ImMunoGeneTics information system®

Acknowledgments

References