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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-24 alpha chain
A
275Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P05534 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P05534
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
C
10Human immunodeficiency virus type 1 group M subtype AMutation(s): 0 
Gene Names: nef
Find proteins for P04603 (Human immunodeficiency virus type 1 group M subtype A)
Go to UniProtKB:  P04603
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.576α = 90.00
b = 78.414β = 90.00
c = 87.278γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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