5HGD

HLA*A2402 complexed with HIV nef138 Y2F mutant 10mer epitope

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation.

Sun, X., Shi, Y., Akahoshi, T., Fujiwara, M., Gatanaga, H., Schonbach, C., Kuse, N., Appay, V., Gao, G.F., Oka, S., Takiguchi, M.

(2016) Cell Rep 15: 2279-2291

  • DOI: 10.1016/j.celrep.2016.05.017
  • Primary Citation of Related Structures:  
    5HGD, 5HGH, 5HGA, 5HGB

  • PubMed Abstract: 

    • The mechanistic basis for the progressive accumulation of Y(135)F Nef mutant viruses in the HIV-1-infected population remains poorly understood. Y(135)F viruses carry the 2F mutation within RW8 and RF10, which are two HLA-A(∗)24:02-restricted superim ...

    The mechanistic basis for the progressive accumulation of Y(135)F Nef mutant viruses in the HIV-1-infected population remains poorly understood. Y(135)F viruses carry the 2F mutation within RW8 and RF10, which are two HLA-A(∗)24:02-restricted superimposed Nef epitopes recognized by distinct and adaptable CD8(+) T cell responses. We combined comprehensive analysis of the T cell receptor repertoire and cross-reactive potential of wild-type or 2F RW8- and RF10-specific CD8(+) T cells with peptide-MHC complex stability and crystal structure studies. We find that, by affecting direct and water-mediated hydrogen bond networks within the peptide-MHC complex, the 2F mutation reduces both TCR and HLA binding. This suggests an advantage underlying the evolution of the 2F variant with decreased CD8(+) T cell efficacy. Our study provides a refined understanding of HIV-1 and CD8(+) T cell co-adaptation at the population level.

    Organizational Affiliation: 

    Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; International Research Center of Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan; Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DS, UK. Electronic address: masafumi@kumamoto-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-24 alpha chainA, D275Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NefC, F10Human immunodeficiency virus 1Mutation(s): 1 
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04601 
Go to UniProtKB:  P04601
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.655α = 67.97
b = 65.741β = 89.8
c = 87.519γ = 89.89
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references, Derived calculations