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

9th of April 2014 release (Database release 201415-3)
- IMGT/3Dstructure-DB contains 3501 entries (2958 PDB, 208 INN and 335 Kabat).
- IMGT/3Dstructure-DB database is now based on a continuous integration process.
25th of March 2013 (Database release 201312-1)
- IMGT/3Dstructure-DB contains 2802 entries (2290 PDB, 177 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB:
      3W11, 3W12, 3W13, 3W14, 3V5K, 4G5Z, 4HC1, 4ENE, 4HCR, 4HGW, 4I9W, 4GRG, 4G6J, 4G6K, 4G6M, 4GBX, 4FQX, 4DVB, 4FFV, 4FFW, 4DW2, 4I0P, 4I4W.
  2. Update of WHO/INN.
    - INN entries from RECOMMENDED International Nonproprietary Names:List 69 are:
      9415, 9567, 9568, 9572, 9575, 9578, 9589, 9590, 9598, 9599, 9608, 9611, 9612, 9620, 9626, 9635, 9647, 9648, 9653.
    - INN entries from Proposed INN: List 108 are:
      9606, 9636, 9643, 9669, 9672, 9679, 9688, 9689, 9703, 9710, 9711, 9713, 9714, 9723, 9724, 9733.
  3. Update of IMGT domain reference directory.
    - Update from the IMGT/GENE-DB database, newly:
      Macaca mulatta IGH, Sus scrofa IGK, Oncorhynchus mykiss MH, Homo sapiens MICA.
18th of October 2012 (Database release 201242-4)
- IMGT/3Dstructure-DB contains 2763 entries (2267 PDB, 161 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 54 PDB).
  2. Update of WHO/INN.
    - INN from Proposed List L106 are available in RECOMMENDED International Nonproprietary Names:List 68
      The concerned INN entries are: 9476,9511,9512,9520,9533,9537,9541,9549.
    - INN from Proposed List L107 are available in
      The concerned INN entries are: 9567,9568,9572,9575,9578,9583,9589,9590,9598,9599,9608,9610,9611,9612,9613,9620,9623,9626,9635,9646,9647,9648,9653.
  3. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus and Macaca mulatta) and from IMGT/HLA-DB database.
5th of March 2012 (Database release 201210-1)
- IMGT/3Dstructure-DB contains 2686 entries (2213 PDB, 137 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 33 PDB).
  2. Update of WHO/INN.
    - INN from Proposed List L105 are available in RECOMMENDED International Nonproprietary Names:List 67
      The concerned INN entries are: 9369,9427,9428,9430,9431,9439,9440,9441,9447,9465,9467,9475,9482,9486,9487.
    - INN from Proposed List L106 are available in
      The concerned INN entries are: 9476,9511,9512,9520,9533,9537,9541,9549.
  3. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus and Macaca mulatta) and from IMGT/HLA-DB database.
19th of October 2011 (Database release 201142-3)
- IMGT/3Dstructure-DB contains 2644 entries (2181 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program.
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 11 PDB). They comprise PDB code 3AU1, 3P4M,,3P4N, 3P4O, 3SCM, 3SDA, 3SDC, 3SDD, 3SDX, 3SKU.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Danio rerio, Oryctolagus cuniculus and Oncorhynchus mykiss) and from IMGT/HLA-DB database.
6th of October 2011 (Database release 201140-4)
- IMGT/3Dstructure-DB contains 2634 entries (2171 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program.
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 11 PDB). They comprise PDB code 2JOP, 2OCW, 2OTT, 2XZA, 2XZC, 3CHN, 3CM9, 3QFD, 3S4S, 3S5L and 3SOB.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus) and from IMGT/HLA-DB database.
    - Addition of S domain sequences (CD5, CD6, CD163, Marco, LOXL2, CfSR and CD163L1 genes)
  3. Addition of specificity for INN entries
    - The specificity in WHO/INN IMGT/2Dstructure-DB cards is available. See as an example WHO/INN entry 8659.
13th of September 2011 (Database release 201137-2)
- IMGT/3Dstructure-DB contains 2623 entries (2160 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program.
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 42 PDB). They comprise PDB code 2PF6, 3AM8, 3AXL, 3AY4, 3NL4, 3NZH, 3O2V, 3O2W, 3O81, 3QOT, 3QPQ, 3QPX, 3QQ9, 3QRG, 3QSK, 3QXV, 3QXW, 3RA7, 3RGV, 3RPI, 3RUG, 3RY6, 3RZC, 3S34, 3S35, 3S36, 3S37, 3SDY, 3SE8, 3SE9, 3SGJ, 3SGK, 3SKJ, 3SM5, 3SN6, 3SY0, 3T4Y, 3T65, 3T77, 3ZTJ and 3ZTN.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Danio rerio, Canus lupus familiaris, Mus musculus) and from IMGT/HLA-DB database.
  3. Addition of specificity for INN entries
    - The specificity in WHO/INN IMGT/2Dstructure-DB cards is now available. See as an example WHO/INN entry 8659.
22nd of July 2011 (Database release 201129-5)
- IMGT/3Dstructure-DB contains 2581 entries (2118 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structure from PDB was entered in IMGT/3Dstructure-DB (Total 1 PDB). It comprises PDB code 3NFN.
  2. Update of WHO/INN Recommended List.
    - INN from Proposed List L104 are available in RECOMMENDED International Nonproprietary Names:List 66
      The concerned INN entries are: 9322, 9334, 9336, 9340, 9343, 9354, 9365, 9368, 9370, 9372, 9373, 9374, 9380, 9290, 9262, 9310, 9382, 9413.
11st of July 2011 (Database release 201128-1)
- IMGT/3Dstructure-DB contains 2580 entries (2117 PDB, 128 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program.
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 56 PDB + 14 INN from Proposed List L105). They comprise PDB code 2XA8, 2XKN, 3MR9, 3MRB, 3MRC, 3MRD, 3MRE, 3MRF, 3MRG, 3MRH, 3MRI, 3MRJ, 3MRK, 3MRL, 3MRM, 3MRN, 3MRO, 3MRP, 3MRQ, 3MRR, 3NFJ, 3NN8, 3NPS, 3NWM, 3NZ8, 3PHO, 3PHQ, 3PJS, 3PQY, 3Q6F, 3Q6G, 3QDA, 3QDG, 3QDJ, 3QDM, 3QEQ, 3QEU, 3QOS, 3QUX, 3QUY, 3QUZ, 3QXT, 3QXU, 3QZW, 3R1G, 3R4D, 3RBG, 3RHW, 3RI5, 3RIA, 3RIF, 3RKD and 3RQ3 and INN code 9427, 9428, 9430, 9431, 9439, 9440, 9441, 9447, 9465, 9467, 9475, 9482, 9486 and 9487.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Mus musculus, Homo sapiens and Danio rerio) and from IMGT/HLA-DB database.
11st of May 2011 (Database release 201119-3)
- IMGT/3Dstructure-DB contains 2513 entries (2064 PDB, 114 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program.
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 56 PDB + 2 INN). They comprise PDB code 2OR8, 2Q87, 2XPG, 2XWT, 2Y7Q, 2YBR, 2YC1, 2YF6, 3ALP, 3ARB, 3ARD, 3ARE, 3ARF, 3ARG, 3CDC, 3EOW, 3LRG, 3LRH, 3M8O, 3MA7, 3NOI, 3O6F, 3OGC, 3OKD, 3OKE, 3OKK, 3OKL, 3OKM, 3OKN, 3OKO, 3PGF, 3PP3, 3PP4, 3PWJ, 3PWL, 3PWN, 3PWP, 3Q5T, 3Q5Y, 3QCT, 3QCU, 3QCV, 3QG6, 3QG7, 3QIB, 3QIU, 3QIW, 3QJF, 3QJH, 3RAJ, 3OX8, 3OXR, 3OXS, 3QWO and INN code 7860 and 8394.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Mus musculus) and from IMGT/HLA-DB database.
  3. 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 (Database release 201109-5)
- IMGT/3Dstructure-DB contains 2457 entries (2010 PDB, 112 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB) and from WHO/INN program (Proposed List L104).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 41 PDB). They comprise PDB code 2X1O, 2X1Q, 2X89, 2XKS, 2XQB, 2XTJ, 3ALX, 3ALZ, 3MCK, 3O0R, 3O4L, 3OAU, 3OAY, 3OAZ, 3OB0, 3OMZ, 3OR6, 3OR7, 3OV6, 3P0G, 3PIQ, 3QHF, 3QHZ and INN code 9262, 9290, 9310, 9322, 9334, 9336, 9340, 9343, 9354, 9365, 9368, 9370.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens and Mus musculus) and from IMGT/HLA-DB database.
30th of December 2010 (Database release 201052-4)
- IMGT/3Dstructure-DB contains 2416 entries (1987 PDB, 94 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 49 PDB). They comprise PDB code 2WQR, 2X70, 2XFX, 2XNA, 2XQY, 2XRA, 3AB0, 3AGV, 3IYW, 3K74, 3K7U, 3K80, 3K81, 3L7E, 3L7F, 3LIZ, 3LN4, 3LN5, 3LN9, 3LV3, 3M45, 3MA9, 3MAC, 3MCL, 3MNV, 3MNW, 3MNZ, 3MO1, 3MOA, 3MOB, 3MOD, 3N9G, 3NH7, 3NID, 3NIF, 3NIG, 3O2D, 3O3A, 3O3B, 3O3D, 3O3E, 3OSK, 3P30, 3P73, 3P77, 3PDO, 3PGC, 3PGD and 3PL6.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus, Canis lupus familiaris and Rattus norvegicus) and from IMGT/HLA-DB database.
8th of November 2010 (Database release 201045-1)
- IMGT/3Dstructure-DB contains 2367 entries (1938 PDB, 94 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 21 PDB). They comprise PDB code 3BEV, 3CFJ, 3JTS, 3JTT, 3KJ4, 3KLH, 3LEV, 3LEX, 3LEY, 3LH2, 3LHP, 3MC0, 3MJ6, 3MJ7, 3NFP, 3NFS, 3O41, 3O45, 3O8X, 3O9W and 3OZ9.
14th of September 2010 (Database release 201037-2)
- IMGT/3Dstructure-DB contains 2346 entries (1917 PDB, 94 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new reference sequences:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 45 PDB). They comprise PDB code 3KG5, 3MYJ, 3NA9, 3NAA, 3NAB, 3NAC, 3NCJ, 3NCY, 3NTC, 3O11, 3OGO and 3OJD.
  2. Update of IMGT/DomainDisplay.
    - Update of the IMGT domain reference directory from the IMGT/GENE-DB database (Homo sapiens, Mus musculus, Oryctolagus cuniculus and Bos taurus) and from IMGT/HLA-DB database.
17th of August 2010 (Database release 201033-2)
- IMGT/3Dstructure-DB contains 2334 entries (1905 PDB, 94 INN and 335 Kabat).
- IMGT/3Dstructure-DB has been upgraded for multiple structures and with new reference sequences:
  1. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 45 PDB). They comprise PDB code 1B09, 1GNH, 1GYK, 1LGN, 1LJ7, 1SAC, 2A3W, 2A3X, 2A3Y, 2W08, 3D5O, 3FB7, 3I6L, 3I75, 3IB4, 3LD8, 3LDB, 3LKN, 3LKO, 3LKP, 3LKQ, 3LKR, 3LKS, 3MLR, 3MLS, 3MLT, 3MLU, 3MLV, 3MLW, 3MLX, 3MLY, 3MLZ, 3N85 and 3NGB.
  2. 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) database.
    - Addition in the IMGT domain reference directory of APCS (serum amyloid P component, SAP) and CRP (C-reactive protein) genes (Homo sapiens).
8th of July 2010 (Database release 201027-4)
- 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 reference sequences:
  1. Addition of sequences from WHO/INN (International Nonproprietary Name).
    - New amino acid sequences from WHO/INN were entered in IMGT/2Dstructure-DB, Proposed List L103 (2010). They comprise INN numbers 9255, 9295, 9299, 9300, 9307, 9308, 9309, 9320, 9321, 9323, 9333 and 9335.
  2. Addition of structures from the Protein Data Bank (PDB).
    - New structures from PDB were entered in IMGT/3Dstructure-DB (Total 45 PDB). They comprise PDB code 2NY7, 2X6M, 2XA3, 3F5W, 3F7V, 3F7Y, 3FB5, 3FB6, 3FB8, 3GO1, 3HMW, 3HMX, 3HPJ, 3HPL, 3HR5, 3I6G, 3I6K, 3IET, 3IF1, 3KDM, 3KR3, 3KS0, 3KWW, 3KXF, 3L6F, 3L9R, 3LRS, 3LS4, 3LS5, 3M17, 3M1B, 3MBE, 3MBX, 3MFF, 3MGO, 3MGT, 3MIQ, 3MME, 3MUG, 3MUH, 3MV7, 3MV8, 3MV9, 3MXV, 3MXW.
  3. 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.

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. (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. (2004) 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. (2005) IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology 5:45-60
[12]	Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc G. (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27:55-77 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. (2005) IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 29:185-203 PMID:15572068
[14]	Lefranc, M.-P., Duprat, E., Kaas, Q., Tranne, M., Thiriot, A. and Lefranc G. (2005) IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily MhcSF G-LIKE-DOMAIN Dev Comp Immunol 29:917-938 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 Database releases

IMGT®, the international ImMunoGeneTics information system®

Acknowledgments

References