7NZE

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

  • 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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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

  • 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. The crystal structures of DRB1*04:01 molecules in complex with the peptides HSP70 289-306 , citrullinated CILP 982-996 and galactosylated Col2 259-273 were determined on cocrystallisation. T cells specific for Col2 259-273 were investigated in peripheral blood mononuclear cells from patients with DRB1*04:01-positive RA by cytofluorometric detection of the activation marker CD154 on peptide stimulation and binding of fluorescent DRB1*0401/Col2 259-273 tetramer complexes. The cDNAs encoding the T-cell receptor (TCR) α-chains and β-chains were cloned from single-cell sorted tetramer-positive T cells and transferred via a lentiviral vector into TCR-deficient Jurkat 76 cells. The crystal structures identified peptide binding to DRB1*04:01 and potential side chain exposure to T cells. The main TCR recognition sites in Col2 259-273 were lysine residues that can be galactosylated. RA T-cell responses to DRB1*04:01-presented Col2 259-273 were dependent on peptide galactosylation at lysine 264. Dynamic molecular modelling of a functionally characterised Col2 259-273 -specific TCR complexed with DRB1*04:01/Col2 259-273 provided evidence for differential allosteric T-cell recognition of glycosylated lysine 264. The MHC-peptide-TCR interactions elucidated in our study provide new molecular insights into recognition of a post-translationally modified RA T-cell determinant with a known dominant role in arthritogenic and tolerogenic responses in murine Col2-induced arthritis.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA [auth AAA],
C [auth CCC]
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01903-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen DR beta chainB [auth BBB],
D [auth DDD]
191Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt
Find proteins for A2BFX2 (Homo sapiens)
Explore A2BFX2 
Go to UniProtKB:  A2BFX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2BFX2
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(II) chainE [auth EEE],
F [auth FFF]
15Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02458
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth AAA],
I [auth BBB],
K [auth CCC]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth AAA],
J [auth BBB],
L [auth DDD],
M [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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 = 122.418α = 90
b = 71.84β = 111.331
c = 125.721γ = 90
Software Package:
Software NamePurpose
REFMACdata reduction
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Swedish Foundation for Strategic ResearchSweden--
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--

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
  • Version 1.3: 2024-11-20
    Changes: Structure summary