9CQ4 | pdb_00009cq4

G115 gamma delta TCR/CD3 complex bound by OKT3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural characterization of two gamma delta TCR/CD3 complexes.

Hoque, M.Grigg, J.B.Ramlall, T.Jones, J.McGoldrick, L.L.Lin, J.C.Olson, W.C.Smith, E.Franklin, M.C.Zhang, T.Saotome, K.

(2025) Nat Commun 16: 318-318

  • DOI: https://doi.org/10.1038/s41467-024-55467-5
  • Primary Citation of Related Structures:  
    9CQ4, 9CQ7, 9CQ8, 9CQL

  • PubMed Abstract: 

    The T-cell receptor (TCR)/CD3 complex plays an essential role in the immune response and is a key player in cancer immunotherapies. There are two classes of TCR/CD3 complexes, defined by their TCR chain usage (αβ or γδ). Recently reported structures have revealed the organization of the αβ TCR/CD3 complex, but similar studies regarding the γδ TCR/CD3 complex have lagged behind. Here, we report cryoelectron microscopy (cryoEM) structural analysis of two γδ TCRs, G115 (Vγ9 Vδ2) and 9C2 (Vγ5 Vδ1), in complex with CD3 subunits. Our results show that the overall subunit organization of the γδ TCR/CD3 complexes is similar to αβ TCRs. However, both γδ TCRs display highly mobile extracellular domains (ECDs), unlike αβ TCRs, which have TCR ECDs that are rigidly coupled to its transmembrane (TM) domains. We corroborate this finding in cells by demonstrating that a γδ T-cell specific antibody can bind a site that would be inaccessible in the more rigid αβ TCR/CD3 complex. Furthermore, we observed that the Vγ5 Vδ1 complex forms a TCR γ5 chain-mediated dimeric species whereby two TCR/CD3 complexes are assembled. Collectively, these data shed light on γδ TCR/CD3 complex formation and may aid the design of γδ TCR-based therapies.


  • Organizational Affiliation
    • Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA. mohammed.hoque@regeneron.com.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OKT3 Fab heavy chainA [auth C],
C [auth H]
238Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OKT3 Fab light chainB [auth D],
D [auth L]
213Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
G115 TCR delta chainE [auth A]283Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
G115 TCR gamma chainF [auth B]295Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainG [auth K]174Homo 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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Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04234-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainH [auth E],
I [auth F]
210Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
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PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainJ [auth G]185Homo 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P09693-1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainK [auth Y],
L [auth Z]
173Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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Oligosaccharides

Help

Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth J]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth O]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release