7RYO

CD1a-dideoxymycobactin-gdTCR complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors.

Wegrecki, M.Ocampo, T.A.Gunasinghe, S.D.von Borstel, A.Tin, S.Y.Reijneveld, J.F.Cao, T.P.Gully, B.S.Le Nours, J.Moody, D.B.Van Rhijn, I.Rossjohn, J.

(2022) Nat Commun 13: 3872-3872

  • DOI: https://doi.org/10.1038/s41467-022-31443-9
  • Primary Citation of Related Structures:  
    7RYL, 7RYM, 7RYN, 7RYO

  • PubMed Abstract: 

    CD1a is a monomorphic antigen-presenting molecule on dendritic cells that presents lipids to αβ T cells. Whether CD1a represents a ligand for other immune receptors remains unknown. Here we use CD1a tetramers to show that CD1a is a ligand for Vδ1 + γδ T cells. Functional studies suggest that two γδ T cell receptors (TCRs) bound CD1a in a lipid-independent manner. The crystal structures of three Vγ4Vδ1 TCR-CD1a-lipid complexes reveal that the γδ TCR binds at the extreme far side and parallel to the long axis of the β-sheet floor of CD1a's antigen-binding cleft. Here, the γδ TCR co-recognises the CD1a heavy chain and β2 microglobulin in a manner that is distinct from all other previously observed γδ TCR docking modalities. The 'sideways' and lipid antigen independent mode of autoreactive CD1a recognition induces TCR clustering on the cell surface and proximal T cell signalling as measured by CD3ζ phosphorylation. In contrast with the 'end to end' binding of αβ TCRs that typically contact carried antigens, autoreactive γδ TCRs support geometrically diverse approaches to CD1a, as well as antigen independent recognition.


  • Organizational Affiliation

    Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD1a286Homo sapiensMutation(s): 2 
Gene Names: CD1A
UniProt & NIH Common Fund Data Resources
Find proteins for P06126 (Homo sapiens)
Explore P06126 
Go to UniProtKB:  P06126
PHAROS:  P06126
GTEx:  ENSG00000158477 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin108Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor gamma variable 4,T cell receptor beta constant 1248Homo sapiensMutation(s): 2 
Gene Names: TRGV4TCRGV4TRBC1
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0C4DH28 (Homo sapiens)
Explore A0A0C4DH28 
Go to UniProtKB:  A0A0C4DH28
GTEx:  ENSG00000211698 
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0C4DH28P01850
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor delta variable 1,T cell receptor alpha chain constant209Homo sapiensMutation(s): 1 
Gene Names: TRDV1TRACTCRA
UniProt & NIH Common Fund Data Resources
Find proteins for A0A1B0GX56 (Homo sapiens)
Explore A0A1B0GX56 
Go to UniProtKB:  A0A1B0GX56
GTEx:  ENSG00000211804 
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP01848A0A1B0GX56
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.881α = 90
b = 42.239β = 113.348
c = 124.656γ = 90
Software Package:
Software NamePurpose
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: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description