7NZE

Crystal structure of HLA-DR4 in complex with a human collagen type II peptide

PDB DOI: https://doi.org/10.2210/pdb7NZE/pdb

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

Deposited: 2021-03-24 Released: 2022-06-08
Deposition Author(s): Ge, C., Dobritzsch, D., Holmdahl, R.
Funding Organization(s): The Swedish Foundation for Strategic Research, Swedish Research Council, Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.245
R-Value Work: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor.

Ge, C., Weisse, S., Xu, B., Dobritzsch, D., Viljanen, J., Kihlberg, J., Do, N.N., Schneider, N., Lanig, H., Holmdahl, R., Burkhardt, H.

(2022) Ann Rheum Dis 81: 480-489

PubMed: 35027402 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1136/annrheumdis-2021-220500
Primary Citation of Related Structures:
7NZE, 7NZF, 7NZH, 7O00

PubMed Abstract:
Rheumatoid arthritis (RA) is an autoimmune disease strongly associated with the major histocompatibility complex (MHC) class II allele DRB1*04:01, which encodes a protein that binds self-peptides for presentation to T cells. This study characterises the autoantigen-presenting function of DRB1*04:01 (HLA-DRA*01:01/HLA-DRB1*04:01) at a molecular level for prototypic T-cell determinants, focusing on a post-translationally modified collagen type II (Col2)-derived peptide.

Organizational Affiliation

Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 91.16 kDa
Atom Count: 6,782
Modelled Residue Count: 770
Deposited Residue Count: 776
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A [auth AAA], C [auth CCC]	182	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903 Go to UniProtKB: P01903
PHAROS: P01903 GTEx: ENSG00000204287
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01903
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B [auth BBB], D [auth DDD]	191	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRB1
UniProt
Find proteins for A2BFX2 (Homo sapiens) Explore A2BFX2 Go to UniProtKB: A2BFX2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2BFX2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(II) chain	E [auth EEE], F [auth FFF]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02458 (Homo sapiens) Explore P02458 Go to UniProtKB: P02458
PHAROS: P02458 GTEx: ENSG00000139219
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02458
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth BBB] SDF format, chain G [auth AAA] SDF format, chain K [auth CCC] MOL2 format, chain I [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain K [auth CCC]	G [auth AAA], I [auth BBB], K [auth CCC]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth AAA] Focus chain I [auth BBB] Focus chain K [auth CCC] Interactions & Density Focus chain G [auth AAA] Focus chain I [auth BBB] Focus chain K [auth CCC]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain J [auth BBB] SDF format, chain L [auth DDD] SDF format, chain M [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain L [auth DDD] MOL2 format, chain M [auth DDD]	H [auth AAA], J [auth BBB], L [auth DDD], M [auth DDD]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain L [auth DDD] Focus chain M [auth DDD] Interactions & Density Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain L [auth DDD] Focus chain M [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.245
R-Value Work: 0.192
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.418	α = 90
b = 71.84	β = 111.331
c = 125.721	γ = 90

Software Package:

Software Name	Purpose
REFMAC	data reduction
REFMAC	refinement
xia2	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-08

Deposition Author(s):

Ge, C.

Dobritzsch, D.

Holmdahl, R.

Funding Organization	Location	Grant Number
The Swedish Foundation for Strategic Research	Sweden	--
Swedish Research Council	Sweden	--
Knut and Alice Wallenberg Foundation	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2022-06-08
Type: Initial release
Version 1.1: 2024-01-03
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-31
Changes: Refinement description