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- EMDB-36147: Extracellular domain of gamma delta TCR -

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Basic information

Entry
Database: EMDB / ID: EMD-36147
TitleExtracellular domain of gamma delta TCR
Map data
Sample
  • Complex: Extracellular domain of gamma delta TCR
    • Protein or peptide: T cell receptor delta variable 1,T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma variable 5,T cell receptor gamma constant 1
KeywordsReceptor / IMMUNE SYSTEM
Function / homology
Function and homology information


gamma-delta T cell receptor complex / gamma-delta T cell activation / T cell receptor complex / small molecule binding / immunoglobulin complex / T cell receptor signaling pathway / adaptive immune response / immune response / innate immune response / external side of plasma membrane / 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)
Methodsingle particle reconstruction / Resolution: 3.02 Å
AuthorsXin W / Chi X / Huang B / Su Q / Zhou Q
Funding support China, 1 items
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, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36147.png

Downloads & links

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Map

FileDownload / File: emd_36147.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.521
Minimum - Maximum-3.5362146 - 5.488895
Average (Standard dev.)-0.0015925192 (±0.090098895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36147_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36147_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Extracellular domain of gamma delta TCR

EntireName: Extracellular domain of gamma delta TCR
Components
  • Complex: Extracellular domain of gamma delta TCR
    • Protein or peptide: T cell receptor delta variable 1,T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma variable 5,T cell receptor gamma constant 1

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Supramolecule #1: Extracellular domain of gamma delta TCR

SupramoleculeName: Extracellular domain of gamma delta TCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: T cell receptor delta variable 1,T cell receptor delta constant
type: protein_or_peptide / ID: 1
Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.320574 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGAQK VTQAQSSVSM PVRKAVTLNC LYETSWWSYY IFWYKQLPSK EMIFLIRQG SDEQNAKSGR YSVNFKKAAK SVALTISALQ LEDSAKYFCA LGDPGGLNTD KLIFGKGTRV TVEPRSQPHT K PSVFVMKN ...String:
MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGAQK VTQAQSSVSM PVRKAVTLNC LYETSWWSYY IFWYKQLPSK EMIFLIRQG SDEQNAKSGR YSVNFKKAAK SVALTISALQ LEDSAKYFCA LGDPGGLNTD KLIFGKGTRV TVEPRSQPHT K PSVFVMKN GTNVACLVKE FYPKDIRINL VSSKKITEFD PAIVISPSGK YNAVKLGKYE DSNSVTCSVQ HDNKTVHSTD FE VKTDSTD HVKPKETENT KQPSKSCHKP KAIVHTEKVN MMSLTVLGLR MLFAKTVAVN FLLTAKLFFL

UniProtKB: T cell receptor delta variable 1, T cell receptor delta constant

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Macromolecule #2: T cell receptor gamma variable 5,T cell receptor gamma constant 1

MacromoleculeName: T cell receptor gamma variable 5,T cell receptor gamma constant 1
type: protein_or_peptide / ID: 2
Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.755172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYYTHT PRRWSWILIL RNLIENDSGV YYCATWDRGN PKTHYYKKLF GSGTTLVVTD K QLDADVSP ...String:
MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYYTHT PRRWSWILIL RNLIENDSGV YYCATWDRGN PKTHYYKKLF GSGTTLVVTD K QLDADVSP KPTIFLPSIA ETKLQKAGTY LCLLEKFFPD VIKIHWQEKK SNTILGSQEG NTMKTNDTYM KFSWLTVPEK SL DKEHRCI VRHENNKNGV DQEIIFPPIK TDVITMDPKD NCSKDANDTL LLQLTNTSAY YMYLLLLLKS VVYFAIITCC LLR RTAFCC NGEKS

UniProtKB: T cell receptor gamma variable 5, T cell receptor gamma constant 1

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 567573
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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