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- PDB-8jbv: Extracellular domain of gamma delta TCR -

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Basic information

Entry
Database: PDB / ID: 8jbv
TitleExtracellular domain of gamma delta TCR
Components
  • T cell receptor delta variable 1,T cell receptor delta constant
  • T cell receptor gamma variable 5,T cell receptor gamma constant 1
KeywordsIMMUNE SYSTEM / Receptor
Function / homology
Function and homology information


gamma-delta T cell receptor complex / gamma-delta T cell activation / T cell receptor complex / small molecule binding / T cell receptor signaling pathway / adaptive immune response / immune response / external side of plasma membrane / innate immune response / extracellular space / plasma membrane
Similarity search - Function
: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor gamma variable 5 / T cell receptor delta variable 1 / T cell receptor delta constant / T cell receptor gamma constant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.02 Å
AuthorsXin, W. / Chi, X. / Huang, B. / Su, Q. / Zhou, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Structures of human γδ T cell receptor-CD3 complex.
Authors: Weizhi Xin / Bangdong Huang / Ximin Chi / Yuehua Liu / Mengjiao Xu / Yuanyuan Zhang / Xu Li / Qiang Su / Qiang Zhou /
Abstract: Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a ...Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex. The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy. Here we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR-CD3 complexes, revealing 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 and connecting peptides. The length of the connecting peptides regulates the ligand association and T cell activation. A cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signalling. The Vγ5Vδ1 TCR-CD3 complex displays a dimeric architecture, whereby two protomers nestle back to back through the Vγ5 domains of the TCR extracellular domains. 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 unique properties of γδ TCR and facilitating immunotherapeutic interventions.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
m: T cell receptor delta variable 1,T cell receptor delta constant
n: T cell receptor gamma variable 5,T cell receptor gamma constant 1
M: T cell receptor delta variable 1,T cell receptor delta constant
N: T cell receptor gamma variable 5,T cell receptor gamma constant 1


Theoretical massNumber of molelcules
Total (without water)144,1514
Polymers144,1514
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein T cell receptor delta variable 1,T cell receptor delta constant


Mass: 34320.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV1, TRDC / Production host: Homo sapiens (human) / References: UniProt: A0A1B0GX56, UniProt: B7Z8K6
#2: Protein T cell receptor gamma variable 5,T cell receptor gamma constant 1


Mass: 37755.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV5, TCRGV5, TRGC1, TCRGC1 / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J1U4, UniProt: P0CF51
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Extracellular domain of gamma delta TCR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 567573 / Symmetry type: POINT

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