2SEB

X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history. 


Literature

X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II.

Dessen, A., Lawrence, C.M., Cupo, S., Zaller, D.M., Wiley, D.C.

(1997) Immunity 7: 473-481

  • DOI: 10.1016/s1074-7613(00)80369-6
  • Primary Citation of Related Structures:  
    2SEB

  • PubMed Abstract: 

    • Genetic predisposition to rheumatoid arthritis (RA) is linked to the MHC class II allele HLA-DR4. The charge of the amino acid at DRbeta71 in the peptide-binding site appears to be critical in discriminating DR molecules linked to increased disease susceptibility ...

    Genetic predisposition to rheumatoid arthritis (RA) is linked to the MHC class II allele HLA-DR4. The charge of the amino acid at DRbeta71 in the peptide-binding site appears to be critical in discriminating DR molecules linked to increased disease susceptibility. We have determined the 2.5 A x-ray structure of the DR4 molecule with the strongest linkage to RA (DRB1*0401) complexed with a human collagen II peptide. Details of a predicted salt bridge between lysine DRbeta71 and aspartic acid at the P4 peptide position suggest how it may participate in both antigen binding and TCR activation. A model is proposed for the DR4 recognition of collagen II (261-273), an antigen immunodominant in human-transgenic mouse models of RA.

    Organizational Affiliation: 

    Laboratory of Molecular Medicine, The Children's Hospital, Boston, Massachusetts 02115, USA. dessen@xtal22.tch.harvard.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGENA181Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
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Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGENB192Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
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Find proteins for P01911 (Homo sapiens)
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Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ENTEROTOXIN TYPE BC [auth D]239Staphylococcus aureusMutation(s): 0 
Gene Names: entB
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UniProt GroupP01552
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE FROM COLLAGEN IID [auth E]12Homo sapiensMutation(s): 0 
Gene Names: COL2A1
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Find proteins for P02458 (Homo sapiens)
Explore P02458 
Go to UniProtKB:  P02458
PHAROS:  P02458
GTEx:  ENSG00000139219 
Entity Groups  
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UniProt GroupP02458
Protein Feature View
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.53α = 90
b = 100.28β = 90
c = 100.87γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary