9O4X | pdb_00009o4x

Gamma delta T cell receptor bound to CD1d

• PDB DOI: https://doi.org/10.2210/pdb9O4X/pdb

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


• Deposited: 2025-04-09 Released: 2025-12-10 
• Deposition Author(s): Rice, M.T., Gully, B.S., Rossjohn, J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

gamma delta T cell receptor bound to CD1d

Rice, M.T., Gully, B.S., Rossjohn, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 92.98 kDa 
• Atom Count: 6,542 
• Modeled Residue Count: 794 
• Deposited Residue Count: 794 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A [auth B]	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor delta chain	B [auth D]	197	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor gamma chain	C [auth G]	224	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	D [auth A]	274	Homo sapiens	Mutation(s): 0  Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813  Go to UniProtKB:  P15813
PHAROS:  P15813 GTEx:  ENSG00000158473
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P15813-1

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F [auth E]	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FO4 (Subject of Investigation/LOI)	H [auth A]	sphingomyelin C47 H94 N2 O6 P NHYQHBPEJLFFSO-QYKFWSDSSA-O
1PE	I [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
NAG	G [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.255 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.093	α = 90
b = 178.093	β = 90
c = 75.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Rice, M.T., Gully, B.S., Rossjohn, J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release