6J29

The structure of HLA-A*3003/MTB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report



Literature

Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides.

Zhu, S.Liu, K.Chai, Y.Wu, Y.Lu, D.Xiao, W.Cheng, H.Zhao, Y.Ding, C.Lyu, J.Lou, Y.Gao, G.F.Liu, W.J.

(2019) Front Immunol 10: 1709-1709

  • DOI: 10.3389/fimmu.2019.01709
  • Primary Citation of Related Structures:  
    6J1V, 6J29, 6J1W, 6J2A

  • PubMed Abstract: 
  • Human leukocyte antigen (HLA) alleles have a high degree of polymorphism, which determines their peptide-binding motifs and subsequent T-cell receptor recognition. The simplest way to understand the cross-presentation of peptides by different alleles ...

    Human leukocyte antigen (HLA) alleles have a high degree of polymorphism, which determines their peptide-binding motifs and subsequent T-cell receptor recognition. The simplest way to understand the cross-presentation of peptides by different alleles is to classify these alleles into supertypes. A1 and A3 HLA supertypes are widely distributed in humans. However, direct structural and functional evidence for peptide presentation features of key alleles (e.g., HLA-A * 30:01 and -A * 30:03) are lacking. Herein, the molecular basis of peptide presentation of HLA-A * 30:01 and -A * 30:03 was demonstrated by crystal structure determination and thermostability measurements of complexes with T-cell epitopes from influenza virus (NP44), human immunodeficiency virus (RT313), and Mycobacterium tuberculosis (MTB). When binding to the HIV peptide, RT313, the PΩ-Lys anchoring modes of HLA-A * 30:01, and -A * 30:03 were similar to those of HLA-A * 11:01 in the A3 supertype. However, HLA-A * 30:03, but not -A * 30:01, also showed binding with the HLA * 01:01-favored peptide, NP44, but with a specific structural conformation. Thus, different from our previous understanding, HLA-A * 30:01 and -A * 30:03 have specific peptide-binding characteristics that may lead to their distinct supertype-featured binding peptide motifs. Moreover, we also found that residue 77 in the F pocket was one of the key residues for the divergent peptide presentation characteristics of HLA-A * 30:01 and -A * 30:03. Interchanging residue 77 between HLA-A * 30:01 and HLA-A * 30:03 switched their presented peptide profiles. Our results provide important recommendations for screening virus and tumor-specific peptides among the population with prevalent HLA supertypes for vaccine development and immune interventions.


    Organizational Affiliation

    NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-A*3003A274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MTBC9Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WNK3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNK3 
Go to UniProtKB:  P9WNK3
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.825α = 90
b = 79.492β = 94.04
c = 44.823γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release