3W39

Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity

Yagita, Y.Kuse, N.Kuroki, K.Gatanaga, H.Carlson, J.M.Chikata, T.Brumme, Z.L.Murakoshi, H.Akahoshi, T.Pfeifer, N.Mallal, S.John, M.Ose, T.Matsubara, H.Kanda, R.Fukunaga, Y.Honda, K.Kawashima, Y.Ariumi, Y.Oka, S.Maenaka, K.Takiguchi, M.

(2013) J.Virol. 87: 2253-2263

  • DOI: 10.1128/JVI.02572-12

  • PubMed Abstract: 
  • Pol283-8-specific, HLA-B*51:01-restricted, cytotoxic T cells (CTLs) play a critical role in the long-term control of HIV-1 infection. However, these CTLs select for the reverse transcriptase (RT) I135X escape mutation, which may be accumulating in ci ...

    Pol283-8-specific, HLA-B*51:01-restricted, cytotoxic T cells (CTLs) play a critical role in the long-term control of HIV-1 infection. However, these CTLs select for the reverse transcriptase (RT) I135X escape mutation, which may be accumulating in circulating HIV-1 sequences. We investigated the selection of the I135X mutation by CTLs specific for the same epitope but restricted by HLA-B*52:01. We found that Pol283-8-specific, HLA-B*52:01-restricted CTLs were elicited predominantly in chronically HIV-1-infected individuals. These CTLs had a strong ability to suppress the replication of wild-type HIV-1, though this ability was weaker than that of HLA-B*51:01-restricted CTLs. The crystal structure of the HLA-B*52:01-Pol283-8 peptide complex provided clear evidence that HLA-B*52:01 presents the peptide similarly to HLA-B*51:01, ensuring the cross-presentation of this epitope by both alleles. Population level analyses revealed a strong association of HLA-B*51:01 with the I135T mutant and a relatively weaker association of HLA-B*52:01 with several I135X mutants in both Japanese and predominantly Caucasian cohorts. An in vitro viral suppression assay revealed that the HLA-B*52:01-restricted CTLs failed to suppress the replication of the I135X mutant viruses, indicating the selection of these mutants by the CTLs. These results suggest that the different pattern of I135X mutant selection may have resulted from the difference between these two CTLs in the ability to suppress HIV-1 replication.


    Organizational Affiliation

    Center for AIDS Research, Kumamoto University, Chuo-ku, Kumamoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-52 alpha chain
A, D
277Homo sapiensGene Names: HLA-B (HLAB)
Find proteins for P30490 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30490
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
100Homo sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptid from Gag-Pol polyprotein
C, F
8Human immunodeficiency virus type 1 group M subtype DGene Names: gag-pol
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D)
Go to UniProtKB:  P12499
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.295 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.045α = 90.00
b = 83.255β = 90.00
c = 170.347γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
RAYONIXdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release