5VGE

Crystal structure of HLA-C*07:02 in complex with RYR peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and regulatory diversity shape HLA-C protein expression levels.

Kaur, G.Gras, S.Mobbs, J.I.Vivian, J.P.Cortes, A.Barber, T.Kuttikkatte, S.B.Jensen, L.T.Attfield, K.E.Dendrou, C.A.Carrington, M.McVean, G.Purcell, A.W.Rossjohn, J.Fugger, L.

(2017) Nat Commun 8: 15924-15924

  • DOI: 10.1038/ncomms15924
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences diff ...

    Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the α1/α2 domains, drives differential expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors that modulate HLA-C expression.


    Organizational Affiliation

    Department of Clinical Medicine, Aarhus University Hospital, 8200N Aarhus, Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cDNA FLJ54183, highly similar to HLA class I histocompatibility antigen, Cw-7 alpha chainA276Homo sapiensMutation(s): 0 
Gene Names: HLA-CHLAC
Find proteins for P10321 (Homo sapiens)
Explore P10321 
Go to UniProtKB:  P10321
NIH Common Fund Data Resources
PHAROS  P10321
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEUC9Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.67α = 90
b = 99.67β = 90
c = 77.914γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references