1SYS

Crystal structure of HLA, B*4403, and peptide EEPTVIKKY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion

Zernich, D.Purcell, A.W.Macdonald, W.A.Kjer-Nielsen, L.Ely, L.K.Laham, N.Crockford, T.Mifsud, N.A.Bharadwaj, M.Chang, L.Tait, B.D.Holdsworth, R.Brooks, A.G.Bottomley, S.P.Beddoe, T.Peh, C.A.Rossjohn, J.McCluskey, J.

(2004) J Exp Med 200: 13-24

  • DOI: 10.1084/jem.20031680
  • Primary Citation of Related Structures:  
    1SYS, 1SYV

  • PubMed Abstract: 
  • HLA class I polymorphism creates diversity in epitope specificity and T cell repertoire. We show that HLA polymorphism also controls the choice of Ag presentation pathway. A single amino acid polymorphism that distinguishes HLA-B*4402 (Asp116) from B*4405 (Tyr116) permits B*4405 to constitutively acquire peptides without any detectable incorporation into the transporter associated with Ag presentation (TAP)-associated peptide loading complex even under conditions of extreme peptide starvation ...

    HLA class I polymorphism creates diversity in epitope specificity and T cell repertoire. We show that HLA polymorphism also controls the choice of Ag presentation pathway. A single amino acid polymorphism that distinguishes HLA-B*4402 (Asp116) from B*4405 (Tyr116) permits B*4405 to constitutively acquire peptides without any detectable incorporation into the transporter associated with Ag presentation (TAP)-associated peptide loading complex even under conditions of extreme peptide starvation. This mode of peptide capture is less susceptible to viral interference than the conventional loading pathway used by HLA-B*4402 that involves assembly of class I molecules within the peptide loading complex. Thus, B*4402 and B*4405 are at opposite extremes of a natural spectrum in HLA class I dependence on the PLC for Ag presentation. These findings unveil a new layer of MHC polymorphism that affects the generic pathway of Ag loading, revealing an unsuspected evolutionary trade-off in selection for optimal HLA class I loading versus effective pathogen evasion.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
leukocyte antigen (HLA) class I moleculeA276Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
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Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo 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 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin 5C9N/AMutation(s): 0 
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Find proteins for Q9Y5X3 (Homo sapiens)
Explore Q9Y5X3 
Go to UniProtKB:  Q9Y5X3
PHAROS:  Q9Y5X3
GTEx:  ENSG00000089006 
Entity Groups  
UniProt GroupQ9Y5X3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.823α = 90
b = 81.985β = 90
c = 110.155γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance