6JXR | pdb_00006jxr

Structure of human T cell receptor-CD3 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.7 of the entry. See complete history

Literature

Structural basis of assembly of the human T cell receptor-CD3 complex.

Zheng, L.Lin, J.Zhang, B.Zhu, Y.Li, N.Xie, S.Wang, Y.Gao, N.Huang, Z.

(2019) Nature 573: 546-552

  • DOI: https://doi.org/10.1038/s41586-019-1537-0
  • Primary Citation Related Structures: 
    6JXR

  • PubMed Abstract: 

    The αβ T cell receptor (TCR), in association with the CD3γε-CD3δε-CD3ζζ signalling hexamer, is the primary determinant of T cell development and activation, and of immune responses to foreign antigens. The mechanism of assembly of the TCR-CD3 complex remains unknown. Here we report a cryo-electron microscopy structure of human TCRαβ in complex with the CD3 hexamer at 3.7 Å resolution. The structure contains the complete extracellular domains and all the transmembrane helices of TCR-CD3. The octameric TCR-CD3 complex is assembled with 1:1:1:1 stoichiometry of TCRαβ:CD3γε:CD3δε:CD3ζζ. Assembly of the extracellular domains of TCR-CD3 is mediated by the constant domains and connecting peptides of TCRαβ that pack against CD3γε-CD3δε, forming a trimer-like structure proximal to the plasma membrane. The transmembrane segment of the CD3 complex adopts a barrel-like structure formed by interaction of the two transmembrane helices of CD3ζζ with those of CD3γε and CD3δε. Insertion of the transmembrane helices of TCRαβ into the barrel-like structure via both hydrophobic and ionic interactions results in transmembrane assembly of the TCR-CD3 complex. Together, our data reveal the structural basis for TCR-CD3 complex assembly, providing clues to TCR triggering and a foundation for rational design of immunotherapies that target the complex.


  • Organizational Affiliation
    • HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.

Macromolecule Content 

  • Total Structure Weight: 184.05 kDa 
  • Atom Count: 8,437 
  • Modeled Residue Count: 1,073 
  • Deposited Residue Count: 1,638 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainA [auth a],
B [auth b]
164Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
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PHAROS:  P20963
GTEx:  ENSG00000198821 
Entity Groups
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UniProt GroupP20963
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Reference Sequence
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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)
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PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainD [auth f],
H [auth e]
207Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
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PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainE [auth g]182Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
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Find proteins for P09693 (Homo sapiens)
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PHAROS:  P09693
GTEx:  ENSG00000160654 
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UniProt GroupP09693
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constantF [auth m]252Homo sapiensMutation(s): 0 
Gene Names: TRAV12-3Tcr-alphaTRACTCRA
Membrane Entity: Yes 
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Find proteins for A0A0B4J271 (Homo sapiens)
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PHAROS:  A0A0B4J271
GTEx:  ENSG00000211794 
Find proteins for A0N4Z6 (Homo sapiens)
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
Entity Groups
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UniProt GroupsA0A0B4J271P01848A0N4Z6
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2G [auth n]291Homo sapiensMutation(s): 0 
Gene Names: TRBV6-5TRBTRBC2
Membrane Entity: Yes 
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Find proteins for A0A0K0K1A5 (Homo sapiens)
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PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
Find proteins for P0DSE2 (Homo sapiens)
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UniProt GroupsP0DSE2A0A0K0K1A5
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.4: 2019-11-06
    Changes: Data collection, Other
  • Version 1.5: 2020-09-16
    Changes: Structure summary
  • Version 1.6: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.7: 2025-06-25
    Changes: Data collection