8VQ8 | pdb_00008vq8

Immune receptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8VQ8

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

LCK-co-receptor association ensures T cell lineage fidelity and maximizes epitope-specific TCR diversity.

Zhang, J.B.Chaurasia, P.Nguyen, A.Huang, Z.Nguyen, T.T.Xu, H.Tran, M.T.Reid, H.H.Jones, C.M.Schattgen, S.A.Thiele, D.Thomas, P.G.Rientjes, J.Good-Jacobson, K.L.Ruscher, R.Littler, D.R.Rossjohn, J.Zareie, P.La Gruta, N.L.

(2025) Sci Immunol 10: eadp5016-eadp5016

  • DOI: https://doi.org/10.1126/sciimmunol.adp5016
  • Primary Citation Related Structures: 
    8VQ8, 9AUD

  • PubMed Abstract: 

    The interaction between the CD4/CD8 co-receptors and LCK (an Src family tyrosine kinase) is thought to augment T cell activation upon recognition of peptide-loaded major histocompatibility complexes (pMHCs). How this interaction influences antigen-specific T cell development is unclear however, as is its impact on naïve and immune antigen-specific T cell repertoires. In mice expressing mutated endogenous LCK unable to bind co-receptors (LCK FREE mice), we show that influenza A virus (IAV)-derived pMHC-specific CD8 and CD4 T cell responses had a significantly narrowed T cell receptor (TCR) repertoire, favoring high-affinity TCRs. This narrowing was established during T cell development and was exacerbated after viral infection. The dissociation of LCK from co-receptors also resulted in the redirection of CD4-fated T cells to the CD8 lineage, with expanded pMHCII-specific cytotoxic CD8 T cells observed after IAV infection. Thus, LCK-co-receptor association is critical for ensuring T cell lineage fidelity and maximizing antigen-specific T cell repertoire diversity.


  • Organizational Affiliation
    • Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.

Macromolecule Content 

  • Total Structure Weight: 99.32 kDa 
  • Atom Count: 6,625 
  • Modeled Residue Count: 777 
  • Deposited Residue Count: 866 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor - LCK1-1 TRAV6-5 alpha chain207Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor - LCK1-1 TRBV1 Beta chain243Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-B alpha chain188Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus)
Explore P14434 
Go to UniProtKB:  P14434
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14434
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain228Influenza A virusMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: NPH2-Ab1H2-iabeta
UniProt
Find proteins for P14483 (Mus musculus)
Explore P14483 
Go to UniProtKB:  P14483
Find proteins for P69296 (Influenza A virus (strain A/Shanghai/16/1989 H3N2))
Explore P69296 
Go to UniProtKB:  P69296
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP14483P69296
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
S [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.604α = 90
b = 197.604β = 90
c = 79.331γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references