6CQN

Crystal structure of F5 TCR -DR11-RQ13 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

CD4+T cell-mediated HLA class II cross-restriction in HIV controllers.

Galperin, M.Farenc, C.Mukhopadhyay, M.Jayasinghe, D.Decroos, A.Benati, D.Tan, L.L.Ciacchi, L.Reid, H.H.Rossjohn, J.Chakrabarti, L.A.Gras, S.

(2018) Sci Immunol 3: --

  • DOI: 10.1126/sciimmunol.aat0687
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rare individuals, termed HIV controllers, spontaneously control HIV infection by mounting efficient T cell responses against the virus. Protective CD4 <sup>+ </sup> T cell responses from HIV controllers involve high-affinity public T cell receptors ( ...

    Rare individuals, termed HIV controllers, spontaneously control HIV infection by mounting efficient T cell responses against the virus. Protective CD4 + T cell responses from HIV controllers involve high-affinity public T cell receptors (TCRs) recognizing an immunodominant capsid epitope (Gag293) presented by a remarkably broad array of human leukocyte antigen (HLA) class II molecules. Here, we determine the structures of a prototypical public TCR bound to HLA-DR1, HLA-DR11, and HLA-DR15 molecules presenting the Gag293 epitope. TCR recognition was driven by contacts with the Gag293 epitope, a feature that underpinned the extensive HLA cross-restriction. These high-affinity TCRs promoted mature immunological synapse formation and cytotoxic capacity in both CD4 + and CD8 + T cells. The public TCRs suppressed HIV replication in multiple genetic backgrounds ex vivo, emphasizing the functional advantage conferred by broad HLA class II cross-restriction.


    Organizational Affiliation

    Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.,Pasteur Institute, Viral Pathogenesis Unit, Paris, France.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,INSERM, U1108, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-11 beta chain
B
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P01911
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide from Capsid protein p24
C
13Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
F5 alpha chain
D
205Homo sapiensMutation(s): 0 
Gene Names: TRAV24
Find proteins for A0A0B4J272 (Homo sapiens)
Go to UniProtKB:  A0A0B4J272
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
F5 beta chain
E
245Homo sapiensMutation(s): 0 
Gene Names: TRBC2
Find proteins for A0A0G2JMB4 (Homo sapiens)
Go to UniProtKB:  A0A0G2JMB4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.317α = 90.00
b = 205.792β = 90.00
c = 70.229γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references, Structure summary