5EO1

Crystal Structure of HLA-B0702-RL9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection.

Du, V.Y., Bansal, A., Carlson, J., Salazar-Gonzalez, J.F., Salazar, M.G., Ladell, K., Gras, S., Josephs, T.M., Heath, S.L., Price, D.A., Rossjohn, J., Hunter, E., Goepfert, P.A.

(2016) J Immunol. 196: 3276-3286

  • DOI: 10.4049/jimmunol.1502411
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Prior work has demonstrated that HIV-1-specific CD8 T cells can cross-recognize variant epitopes. However, most of these studies were performed in the context of chronic infection, where the presence of viral quasispecies makes it difficult to ascert ...

    Prior work has demonstrated that HIV-1-specific CD8 T cells can cross-recognize variant epitopes. However, most of these studies were performed in the context of chronic infection, where the presence of viral quasispecies makes it difficult to ascertain the true nature of the original antigenic stimulus. To overcome this limitation, we evaluated the extent of CD8 T cell cross-reactivity in patients with acute HIV-1 clade B infection. In each case, we determined the transmitted founder virus sequence to identify the autologous epitopes restricted by individual HLA class I molecules. Our data show that cross-reactive CD8 T cells are infrequent during the acute phase of HIV-1 infection. Moreover, in the uncommon instances where cross-reactive responses were detected, the variant epitopes were poorly recognized in cytotoxicity assays. Molecular analysis revealed that similar antigenic structures could be cross-recognized by identical CD8 T cell clonotypes mobilized in vivo, yet even subtle differences in a single TCR-accessible peptide residue were sufficient to disrupt variant-specific reactivity. These findings demonstrate that CD8 T cells are highly specific for autologous epitopes during acute HIV-1 infection. Polyvalent vaccines may therefore be required to provide optimal immune cover against this genetically labile pathogen.

    Organizational Affiliation: 

    Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-7 alpha chain
A
275Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P01889 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P01889
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
RL9 peptide
C
9Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)Mutation(s): 0 
Gene Names: nef
Find proteins for P12478 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Go to UniProtKB:  P12478
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.662α = 90.00
b = 81.857β = 90.00
c = 110.366γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2016-04-20
    Type: Database references