4MJI

T cell response to a HIV reverse transcriptase epitope presented by the protective allele HLA-B*51:01

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Molecular basis of a dominant T cell response to an HIV reverse transcriptase 8-mer epitope presented by the protective allele HLA-B*51:01

Motozono, C., Kuse, N., Sun, X., Rizkallah, P.J., Fuller, A., Oka, S., Cole, D.K., Sewell, A.K., Takiguchi, M.

(2014) J.Immunol. 192: 3428-3434

  • DOI: 10.4049/jimmunol.1302667

  • PubMed Abstract: 

    • CD8(+) CTL responses directed toward the HLA-B*51:01-restricted HIV-RT128-135 epitope TAFTIPSI (TI8) are associated with long-term nonprogression to AIDS. Clonotypic analysis of responses to B51-TI8 revealed a public clonotype using TRAV17/TRBV7-3 TC ...

    CD8(+) CTL responses directed toward the HLA-B*51:01-restricted HIV-RT128-135 epitope TAFTIPSI (TI8) are associated with long-term nonprogression to AIDS. Clonotypic analysis of responses to B51-TI8 revealed a public clonotype using TRAV17/TRBV7-3 TCR genes in six out of seven HLA-B*51:01(+) patients. Structural analysis of a TRAV17/TRBV7-3 TCR in complex with HLA-B51-TI8, to our knowledge the first human TCR complexed with an 8-mer peptide, explained this bias, as the unique combination of residues encoded by these genes was central to the interaction. The relatively featureless peptide-MHC (pMHC) was mainly recognized by the TCR CDR1 and CDR2 loops in an MHC-centric manner. A highly conserved residue Arg(97) in the CDR3α loop played a major role in recognition of peptide and MHC to form a stabilizing ball-and-socket interaction with the MHC and peptide, contributing to the selection of the public TCR clonotype. Surface plasmon resonance equilibrium binding analysis showed the low affinity of this public TCR is in accordance with the only other 8-mer interaction studied to date (murine 2C TCR-H-2K(b)-dEV8). Like pMHC class II complexes, 8-mer peptides do not protrude out the MHC class I binding groove like those of longer peptides. The accumulated evidence suggests that weak affinity might be a common characteristic of TCR binding to featureless pMHC landscapes.

    Organizational Affiliation: 

    Cardiff University School of Medicine, Heath Park CF14 4XN, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-51 alpha chain
A, F
276Homo 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, G
99Homo 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
HIV Reverse Transcriptase peptide Marker
C, H
8Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for R4WL38 (Human immunodeficiency virus 1)
Go to UniProtKB:  R4WL38
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-Cell Receptor Chain alpha
D, I
195Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for K7N5M3 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  K7N5M3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
T-cell Receptor Beta chain
E, J
242Homo sapiensMutation(s): 0 
Gene Names: TRBC1
Find proteins for P01850 (Homo sapiens)
Go to UniProtKB:  P01850
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.242 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.510α = 102.91
b = 88.870β = 95.92
c = 129.270γ = 90.09
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release