1I4F | pdb_00001i4f

CRYSTAL STRUCTURE OF HLA-A*0201/MAGE-A4-PEPTIDE COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1I4F/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-02-21 Released: 2001-07-25
Deposition Author(s): Hillig, R.C., Coulie, P.G., Stroobant, V., Saenger, W., Ziegler, A., Huelsmeyer, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.173 (Depositor), 0.176 (DCC)
R-Value Work:
0.136 (Depositor), 0.140 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

High-resolution structure of HLA-A*0201 in complex with a tumour-specific antigenic peptide encoded by the MAGE-A4 gene.

Hillig, R.C., Coulie, P.G., Stroobant, V., Saenger, W., Ziegler, A., Hulsmeyer, M.

(2001) J Mol Biology 310: 1167-1176

PubMed: 11502003 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.2001.4816
Primary Citation Related Structures:
1I4F

PubMed Abstract:
The heterotrimeric complex of the human major histocompatibity complex (MHC) molecule HLA-A*0201, beta2-microglobulin and the decameric peptide GVYDGREHTV derived from the melanoma antigen (MAGE-A4 protein has been determined by X-ray crystallography at 1.4 A resolution. MAGE-A4 belongs to a family of genes that are specifically expressed in a variety of tumours. MAGE-A4-derived peptides are presented by MHC molecules at the cell surface to cytotoxic T-lymphocytes. As the HLA-A*0201:MAGE-A4 complex occurs only on tumour cells, it is considered to be an appropriate target for immunotherapy. The structure presented here reveals potential epitopes specific to the complex and indicates which peptide residues could be recognised by T-cell receptors. In addition, as the structure could be refined anisotropically, it was possible to describe the movements of the bound peptide in more detail.

Organizational Affiliation

Institut für Immungenetik, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Germany.

Macromolecule Content

Total Structure Weight: 45.37 kDa
Atom Count: 3,704
Modeled Residue Count: 385
Deposited Residue Count: 385
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN	A	275	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-MICROGLOBULIN	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MELANOMA-ASSOCIATED ANTIGEN 4	C	10	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P43358 (Homo sapiens) Explore P43358 Go to UniProtKB: P43358
PHAROS: P43358 GTEx: ENSG00000147381
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43358
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG Query on 1PG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.173 (Depositor), 0.176 (DCC)
R-Value Work: 0.136 (Depositor), 0.140 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.467	α = 90
b = 80.222	β = 111.06
c = 54.009	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2001-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-07-25
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary