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

Program version:
4.12.2 (2016-10-10)
Database release:
201639-1 (2016-09-26)
Citing IMGT/3Dstructure-DB:
Kaas, Q. et al. Nucleic Acids Res., 32, D208 - D210 (2004). PMID: 14681396 Abstract Full pdf
Ehrenmann, F. et al. Nucleic Acids Res., 38, D301 - D307 (2010). PMID: 19900967 Abstract Full pdf

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)

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.

Definitions

A Chimeric receptor is one of which all chains are chimeric as a result of protein engineering. A chimeric chain is a chain that contains a foreign region (originating from one species other than human, or synthetic) linked to another region of different species. Note that the definition of a chimeric antibody is more precise.

A Humanized receptor is one of which all chains are humanized as a result of protein engineering. A humanized chain is a chain in which a region is foreign (originating from one species other than human, or synthetic) whereas the remaining chain is of human origin. Note that the definition of a humanized antibody is more precise. 'Camelized', 'Chimeric', 'Humanized' and 'Synthetic' refer to both the receptor and to its chain(s).

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).

IMGT Complex type

Search by Complex type can retrieve entries similar to the following complexes:

Ligand category

Search by Ligand category can retrieve structures which are in contacts with: Carbohydrate, Chemical compound, DNA, peptide, Protein or RNA.

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.

IMGT description rules

IMGT receptor and chain description is based on the IMGT-ONTOLOGY DESCRIPTION concept.

IG, TR, MH or RPI receptors and chains are described with standardized labels (listed in IMGT/PROTEIN-DB and IMGT/3Dstructure-DB: standardized keywords and labels for IG, TR and MH), and defined in the IMGT Scientific chart (IMGT/PROTEIN-DB and IMGT/3Dstructure-DB: Label definitions for IG, TR and MH).

If the receptor is incomplete, the receptor label is replaced by domain or chain labels shown between parentheses.

IMGT classification rules:

Group, subgroup, gene and allele names are based on the IMGT-ONTOLOGY CLASSIFICATION concept.

Gene:

IG and TR: V-GENE, D-GENE, J-GENE and C-GENE names are according to the IMGT gene nomenclature. Human and mouse IG and TR genes are from IMGT/GENE-DB. The D-GENE identification is not shown when it is too uncertain owing to the shortness of the D sequences in the V-D-J rearrangement, to N-region diversity and/or, for the IG, to somatic hypermutations.

MH: The closest gene(s) is (are) provided for the rodent MH.

Allele:

IG and TR: The closest allele(s) is (are) provided for each gene. Human and mouse alleles are from IMGT/GENE-DB. Alleles are displayed in IMGT Alignments of alleles and IMGT/DomainDisplay.

MH: The closest allele(s) is (are) provided for the human MH (HLA).

Search by Position

The form allows an easy search by the following criteria:

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:

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. TRAV_CDR3=13
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). CDR1=8_AAV=29V

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

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:

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:

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:

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:

For INN entries, a summary table with:

Below the summary table are added:

Identification of the chains belonging to the same protein quaternary structure

Chains belong to the same protein quaternary structure when they are of the same type (IG, TR, MH or else), their amino acid sequence length is of the same order (no peptide with huge protein) and have at least 60 amino acids contacts and eventually a covalent link (as identified by the coordinate file). A manual expertise is sometimes required to correct errors created by these very simple rules and in some intricate cases.

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

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.

Domain description of a chain

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

The display includes, for each domain:

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

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

Carbohydrate chains and molecules of particular interest

Although carbohydrates are usually linked covalently to the amino acid chains, they are considered separately as a carbohydrate chain from the amino acid chain in the IMGT/3Dstructure-DB card.

IMGT chain ID is assigned to molecules of particular interest (for example inorganic antigene, heme molecule, etc.). This allows to distinguish these molecules from solvant and ions and to view them in the IMGT/3Dstructure-DB card summary table and in the IMGT/3Dstructure-DB contact analysis cards.

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

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.

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 Jmol or QuickPDB

3D visualization with Jmol

The whole chain sequences are displayed in a box, indicating the 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).

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

The Selection menu offers a selection by:

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:

The Coloration menu offers a display:

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

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

3D visualization with QuickPDB

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

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:

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 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) and Patrice Duroux (LIGM, Montpellier, France)