3WL9

HLA-A24 in complex with HIV-1 Nef126-10(8I10F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Switching and emergence of CTL epitopes in HIV-1 infection

Han, C.Kawana-tachikawa, A.Shimizu, A.Zhu, D.Nakamura, H.Adachi, E.Kikuchi, T.Koga, M.Koibuchi, T.Gao, G.F.Sato, Y.Yamagata, A.Martin, E.Fukai, S.Brumme, Z.L.Iwamoto, A.

(2014) Retrovirology 11: 38-38

  • DOI: 10.1186/1742-4690-11-38
  • Primary Citation of Related Structures:  
    3WLB, 3WL9

  • PubMed Abstract: 
  • Human Leukocyte Antigen (HLA) class I restricted Cytotoxic T Lymphocytes (CTLs) exert substantial evolutionary pressure on HIV-1, as evidenced by the reproducible selection of HLA-restricted immune escape mutations in the viral genome. An escape muta ...

    Human Leukocyte Antigen (HLA) class I restricted Cytotoxic T Lymphocytes (CTLs) exert substantial evolutionary pressure on HIV-1, as evidenced by the reproducible selection of HLA-restricted immune escape mutations in the viral genome. An escape mutation from tyrosine to phenylalanine at the 135th amino acid (Y135F) of the HIV-1 nef gene is frequently observed in patients with HLA-A*24:02, an HLA Class I allele expressed in ~70% of Japanese persons. The selection of CTL escape mutations could theoretically result in the de novo creation of novel epitopes, however, the extent to which such dynamic "CTL epitope switching" occurs in HIV-1 remains incompletely known.


    Organizational Affiliation

    Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. aikichi@ra3.so-net.ne.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chainA275Homo 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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
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 LengthOrganismDetailsImage
Protein NefC10Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for P04603 (Human immunodeficiency virus type 1 group M subtype A (isolate MAL))
Explore P04603 
Go to UniProtKB:  P04603
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.576α = 90
b = 78.414β = 90
c = 87.278γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description