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- EMDB-39950: Cryo-EM structure of the gdTCR-ECD -

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Basic information

Entry
Database: EMDB / ID: EMD-39950
TitleCryo-EM structure of the gdTCR-ECD
Map data
Sample
  • Complex: TCR-CD3
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain
Keywordscomplex / immune / IMMUNE SYSTEM
Function / homology
Function and homology information


T cell receptor complex / adaptive immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBai Y / Zhu Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunity / Year: 2025
Title: Phosphoantigen-induced inside-out stabilization of butyrophilin receptor complexes drives dimerization-dependent γδ TCR activation.
Authors: Yuwei Zhu / Wenbo Gao / Jianlin Zheng / Ye Bai / Xinyu Tian / Tengjin Huang / Zebin Lu / De Dong / Anqi Zhang / Changyou Guo / Zhiwei Huang /
Abstract: Phosphoantigens (pAgs), produced by infected or cancer cells, trigger the assembly of a membrane receptor complex comprising butyrophilin (BTN) members BTN3A1 and BTN2A1, leading to the activation of ...Phosphoantigens (pAgs), produced by infected or cancer cells, trigger the assembly of a membrane receptor complex comprising butyrophilin (BTN) members BTN3A1 and BTN2A1, leading to the activation of γδ T cells. BTN3A2 or BTN3A3 forms heteromers with BTN3A1, exhibiting higher γδ T cell receptor (TCR)-stimulating activity than BTN3A1 homomers. Cryoelectron microscopy (cryo-EM) structure reveals a pAg-induced BTN2A1-BTN3A1 heterotetramer with a 2:2 stoichiometry, stabilized by interactions between the intracellular B30.2 domains and the extracellular immunoglobulin V (IgV) domains. BTN3A2 or BTN3A3 heterodimerizes with BTN3A1, forming a pAg-induced tetrameric complex with BTN2A1. However, BTN3A1 heterodimers are more stable than BTN3A1 homodimers in this interaction. Cryo-EM reveals that BTN2A1-BTN3A1-BTN3A2 binds two γδ TCR ectodomains, with one being sandwiched between the IgV domains of BTN2A1 and BTN3A2, while the other interacts with the free BTN2A1 IgV in the complex, as evidenced by functional data. Together, our findings uncover the mechanism of ligand-induced inside-out stabilization of BTN receptor complexes for dimeric activation of γδ TCR.
History
DepositionMay 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39950.png

Downloads & links

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Map

FileDownload / File: emd_39950.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.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-5.338356 - 8.274853
Average (Standard dev.)-0.0024834792 (±0.10621506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39950_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39950_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : TCR-CD3

EntireName: TCR-CD3
Components
  • Complex: TCR-CD3
    • Protein or peptide: TRA@ protein
    • Protein or peptide: gamma chain

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Supramolecule #1: TCR-CD3

SupramoleculeName: TCR-CD3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TRA@ protein

MacromoleculeName: TRA@ protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.652867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKVTQAQSSV SMPVRKAVTL NCLYETSWWS YYIFWYKQLP SKEMIFLIRQ GSDEQNAKSG RYSVNFKKAA KSVALTISAL QLEDSAKYF CALGDPGGLN TDKLIFGKGT RVTVEPRSQP HTKPSVFVMK NGTNVACLVK EFYPKDIRIN LVSSKKITEF D PAIVISPS ...String:
QKVTQAQSSV SMPVRKAVTL NCLYETSWWS YYIFWYKQLP SKEMIFLIRQ GSDEQNAKSG RYSVNFKKAA KSVALTISAL QLEDSAKYF CALGDPGGLN TDKLIFGKGT RVTVEPRSQP HTKPSVFVMK NGTNVACLVK EFYPKDIRIN LVSSKKITEF D PAIVISPS GKYNAVKLGK YEDSNSVTCS VQHDNKTVHS TDFE

UniProtKB: TRA@ protein, TRA@ protein

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Macromolecule #2: gamma chain

MacromoleculeName: gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.888461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTKSVTRPTR SSAEITCDLT VINAFYIHWY LHQEGKAPQR LLYYDVSNSK DVLESGLSPG KYYTHTPRRW SWILILRNLI ENDSGVYYC ATWDRGNPKT HYYKKLFGSG TTLVVTDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL EKFFPDVIKI H WQEKKSNT ...String:
GTKSVTRPTR SSAEITCDLT VINAFYIHWY LHQEGKAPQR LLYYDVSNSK DVLESGLSPG KYYTHTPRRW SWILILRNLI ENDSGVYYC ATWDRGNPKT HYYKKLFGSG TTLVVTDKQL DADVSPKPTI FLPSIAETKL QKAGTYLCLL EKFFPDVIKI H WQEKKSNT ILGSQEGNTM KTNDTYMKFS WLTVPEESLD KEHRCIVRHE NNKNGVDQEI IFPPIK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1535676
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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