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 ?
  • R-Value Free: 
    0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.200 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


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) ¦Á-chains and ¦Â-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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

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
Expand
  • 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 ?
  • R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 122.418¦Á = 90
b = 71.84¦Â = 111.331
c = 125.721¦Ã = 90
Software Package:
Software NamePurpose
REFMACdata reduction
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



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
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