9JXZ | pdb_00009jxz

V gamma9 V delta2 TCR and CD3 complex

PDB DOI: https://doi.org/10.2210/pdb9JXZ/pdb
EM Map EMD-61882: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-10-12 Released: 2025-10-22
Deposition Author(s): Wang, L., Li, J., Li, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structures of the apo and agonist-crosslinked human gamma delta T-cell receptor

Wang, L., Li, Z., Fan, Y., Li, J.

To be published.

Macromolecule Content

Total Structure Weight: 193.92 kDa
Atom Count: 4,846
Modeled Residue Count: 597
Deposited Residue Count: 1,706
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 zeta chain	A [auth a], B [auth b]	166	Homo sapiens	Mutation(s): 0 Gene Names: CD247, CD3Z, T3Z, TCRZ
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens) Explore P20963 Go to UniProtKB: P20963
PHAROS: P20963 GTEx: ENSG00000198821
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20963
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 delta chain	C [auth d]	171	Homo sapiens	Mutation(s): 0 Gene Names: CD3D, T3D
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens) Explore P04234 Go to UniProtKB: P04234
PHAROS: P04234 GTEx: ENSG00000167286
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04234
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 epsilon chain	D [auth e], E [auth f]	207	Homo sapiens	Mutation(s): 0 Gene Names: CD3E, T3E
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens) Explore P07766 Go to UniProtKB: P07766
PHAROS: P07766 GTEx: ENSG00000198851
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD3 gamma chain	F [auth g]	182	Homo sapiens	Mutation(s): 0 Gene Names: CD3G, T3G
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens) Explore P09693 Go to UniProtKB: P09693
PHAROS: P09693 GTEx: ENSG00000160654
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09693
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor delta variable 2,T cell receptor delta constant	G [auth m]	292	Homo sapiens	Mutation(s): 0 Gene Names: TRDV2, hDV102S1, TRDC
UniProt
Find proteins for B7Z8B9 (Homo sapiens) Explore B7Z8B9 Go to UniProtKB: B7Z8B9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7Z8B9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor gamma variable 9,T cell receptor gamma constant 1	H [auth n]	315	Homo sapiens	Mutation(s): 0 Gene Names: TRGV9, TCRGV9, TRGC1, TCRGC1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CF51 (Homo sapiens) Explore P0CF51 Go to UniProtKB: P0CF51
Find proteins for Q99603 (Homo sapiens) Explore Q99603 Go to UniProtKB: Q99603
GTEx: ENSG00000211695
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q99603P0CF51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPE (Subject of Investigation/LOI) Query on LPE Download Ideal Coordinates CCD File SDF format, chain J [auth b] SDF format, chain K [auth b] SDF format, chain M [auth d] MOL2 format, chain J [auth b] MOL2 format, chain K [auth b] MOL2 format, chain M [auth d] mmCIF format, chain J [auth b] mmCIF format, chain K [auth b] mmCIF format, chain M [auth d]	J [auth b], K [auth b], M [auth d]	1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₂₆ H₅₇ N O₆ P XKBJVQHMEXMFDZ-AREMUKBSSA-O		Interactions Focus chain J [auth b] Focus chain K [auth b] Focus chain M [auth d] Interactions & Density Focus chain J [auth b] Focus chain K [auth b] Focus chain M [auth d]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain I [auth b] SDF format, chain L [auth b] MOL2 format, chain I [auth b] MOL2 format, chain L [auth b] mmCIF format, chain I [auth b] mmCIF format, chain L [auth b]	I [auth b], L [auth b]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth b] Focus chain L [auth b] Interactions & Density Focus chain I [auth b] Focus chain L [auth b]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Wang, L.

Li, J.

Li, Z.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release
Version 1.1: 2025-11-05
Changes: Data collection, Database references, Source and taxonomy, Structure summary