6CQQ

Crystal structure of F24 TCR -DR15-RQ13 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 ( ...

    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

    ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA-DRB1 protein
B, G
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS  P01911

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
F24 beta chain
E, J
245Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, F
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
Find proteins for P01903 (Homo sapiens)
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide from Capsid protein p24
C, H
13HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04591

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
F24 alpha chain
D, I
205Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, F, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
J
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.339α = 90
b = 203.273β = 109.16
c = 100.245γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Derived calculations
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references, Structure summary