5W6A

HLA-C*06:02 presenting ARTELYRSL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule.

Mobbs, J.I.Illing, P.T.Dudek, N.L.Brooks, A.G.Baker, D.G.Purcell, A.W.Rossjohn, J.Vivian, J.P.

(2017) J Biol Chem 292: 17203-17215

  • DOI: https://doi.org/10.1074/jbc.M117.806976
  • Primary Citation of Related Structures:  
    5W67, 5W69, 5W6A

  • PubMed Abstract: 

    Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.


  • Organizational Affiliation

    From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, Cw-6 alpha chain
A, C
276Homo sapiensMutation(s): 0 
Gene Names: HLA-CHLAC
UniProt & NIH Common Fund Data Resources
Find proteins for P10321 (Homo sapiens)
Explore P10321 
Go to UniProtKB:  P10321
PHAROS:  P10321
GTEx:  ENSG00000204525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10321
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ARG-THR-GLU-LEU-TYR-ARG-SER-LEU
E, F
9synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY61 (Homo sapiens)
Explore Q9NY61 
Go to UniProtKB:  Q9NY61
PHAROS:  Q9NY61
GTEx:  ENSG00000275700 
Entity Groups  
UniProt GroupQ9NY61
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.191α = 90
b = 136.95β = 107.06
c = 70.961γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description