9CIA | pdb_00009cia

T cell receptor complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a fully assembled gamma delta T cell antigen receptor.

Gully, B.S.Ferreira Fernandes, J.Gunasinghe, S.D.Vuong, M.T.Lui, Y.Rice, M.T.Rashleigh, L.Lay, C.S.Littler, D.R.Sharma, S.Santos, A.M.Venugopal, H.Rossjohn, J.Davis, S.J.

(2024) Nature 634: 729-736

  • DOI: https://doi.org/10.1038/s41586-024-07920-0
  • Primary Citation of Related Structures:  
    9CI8, 9CIA

  • PubMed Abstract: 

    T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands 1 . Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood 2,3 , the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR-CD3δγε 2 ζ 2 complex bound by anti-CD3ε antibody Fab fragments 4,5 . The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR 2,3,6 , the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.


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

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UCHT1 Fab 2
A, C
107Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UCHT1 Fab chain
B, D
120Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainE [auth a],
F [auth b]
29Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainG [auth e],
H [auth f]
123Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
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GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor delta constantI [auth m]35Homo sapiensMutation(s): 0 
Gene Names: TRDC
Membrane Entity: Yes 
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UniProt GroupB7Z8K6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor gamma constant 1J [auth n]36Homo sapiensMutation(s): 0 
Gene Names: TRGC1TCRGC1
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainK [auth d]106Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
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GTEx:  ENSG00000167286 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainL [auth g]114Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
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PHAROS:  P09693
GTEx:  ENSG00000160654 
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UniProt GroupP09693
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
M [auth b]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARCv4.2.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP230102073

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-09-03
    Changes: Data collection, Database references