3W39

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.298 

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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
  • Primary Citation of Related Structures:  
    3W39

  • 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 circulating HIV-1 sequences ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-52 alpha chainAD277Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
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PHAROS  P01889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinBE100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
peptid from Gag-Pol polyproteinCF8Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)Mutation(s): 0 
Gene Names: gag-pol
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Explore P12499 
Go to UniProtKB:  P12499
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.298 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.045α = 90
b = 83.255β = 90
c = 170.347γ = 90
Software Package:
Software NamePurpose
RAYONIXdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History 

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