7O00

Crystal structure of HLA-DR4 in complex with a HSP70 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 

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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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA [auth AAA]177Homo 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
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]189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt
Find proteins for A0A1V1IGJ9 (Homo sapiens)
Explore A0A1V1IGJ9 
Go to UniProtKB:  A0A1V1IGJ9
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UniProt GroupA0A1V1IGJ9
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaKC [auth CCC]14Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WMJ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMJ9 
Go to UniProtKB:  P9WMJ9
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UniProt GroupP9WMJ9
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth AaA]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth BBB]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.23α = 90
b = 76.23β = 90
c = 170.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
XDSdata reduction
XDSdata 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: 2022-05-11
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description