8JC0 | pdb_00008jc0

V gamma9 V delta2 TCR and CD3 complex in LMNG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8JC0

This is version 1.2 of the entry. See complete history

Literature

Structures of human gamma delta T cell receptor-CD3 complex.

Xin, W.Huang, B.Chi, X.Liu, Y.Xu, M.Zhang, Y.Li, X.Su, Q.Zhou, Q.

(2024) Nature 630: 222-229

  • DOI: https://doi.org/10.1038/s41586-024-07439-4
  • Primary Citation Related Structures: 
    8JBV, 8JC0, 8JCB, 8WXE, 8WY0, 8WYI, 8YC0

  • PubMed Abstract: 

    Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology 1-3 . The γδ T cell receptor (TCR), generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex 2 . The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy 4 . Here, we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR-CD3 complexes 5,6 , unveiling two distinct assembly mechanisms that depend on Vγ usage. The Vγ9Vδ2 TCR-CD3 complex is monomeric, with considerable conformational flexibility in the TCRγ/TCRδ extracellular domain (ECD) and connecting peptides (CPs). The length of CPs regulates the ligand association and T cell activation. Additionally, a cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signaling. The Vγ5Vδ1 TCR-CD3 complex displays a dimeric architecture, where two protomers nestle back-to-back via their Vγ5 domains of TCR ECDs. Our biochemical and biophysical assays further corroborate the dimeric structure. Importantly, the dimeric form of the Vγ5Vδ1 TCR is essential for T cell activation. These findings reveal organizing principles of the γδ TCR-CD3 complex, providing insights into the γδ TCR unique properties and facilitating immunotherapeutic interventions.


  • Organizational Affiliation
    • Research Center for Industries of the Future, Center for Infectious Disease Research, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.

Macromolecule Content 

  • Total Structure Weight: 201.76 kDa 
  • Atom Count: 4,691 
  • Modeled Residue Count: 589 
  • Deposited Residue Count: 1,799 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainA [auth a],
B [auth b]
195Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
Explore P20963 
Go to UniProtKB:  P20963
PHAROS:  P20963
GTEx:  ENSG00000198821 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20963
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainC [auth d]171Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
Explore P04234 
Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04234
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainD [auth e],
E [auth f]
207Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
Explore P07766 
Go to UniProtKB:  P07766
PHAROS:  P07766
GTEx:  ENSG00000198851 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07766
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainF [auth g]182Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens)
Explore P09693 
Go to UniProtKB:  P09693
PHAROS:  P09693
GTEx:  ENSG00000160654 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09693
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor delta variable 2,T cell receptor delta constantG [auth m]310Homo sapiensMutation(s): 0 
Gene Names: TRDV2hDV102S1TRDC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for A0JD36 (Homo sapiens)
Explore A0JD36 
Go to UniProtKB:  A0JD36
GTEx:  ENSG00000211821 
Find proteins for B7Z8K6 (Homo sapiens)
Explore B7Z8K6 
Go to UniProtKB:  B7Z8K6
PHAROS:  B7Z8K6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0JD36B7Z8K6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor gamma variable 9,T cell receptor gamma constant 1H [auth n]332Homo sapiensMutation(s): 0 
Gene Names: TRGV9TCRGV9TRGC1TCRGC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CF51 (Homo sapiens)
Explore P0CF51 
Go to UniProtKB:  P0CF51
Find proteins for Q99603 (Homo sapiens)
Explore Q99603 
Go to UniProtKB:  Q99603
GTEx:  ENSG00000211695 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ99603P0CF51
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
(Subject of Investigation/LOI)

Query on CLR



Download:Ideal Coordinates CCD File
I [auth m]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32022037
National Natural Science Foundation of China (NSFC)China82241081

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary