9SOK | pdb_00009sok

Structure of three-domain single chain TCR-581 in complex with Peptide-HLA

• PDB DOI: https://doi.org/10.2210/pdb9SOK/pdb

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


• Deposited: 2025-09-14 Released: 2026-09-16 
• Deposition Author(s): Karuppiah, V.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.262 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Models: experimental

Literature

Isolation of Human TCRs specific to any peptide-HLA complex

Karuppiah, V.

(2026) Nat Commun 

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: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 87.43 kDa 
• Atom Count: 6,054 
• Modeled Residue Count: 736 
• Deposited Residue Count: 767 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A5B8RNS7 (Homo sapiens) Explore A0A5B8RNS7  Go to UniProtKB:  A0A5B8RNS7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi-like protein 1	C	9	Homo sapiens	Mutation(s): 0  EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q96J94 (Homo sapiens) Explore Q96J94  Go to UniProtKB:  Q96J94
PHAROS:  Q96J94 GTEx:  ENSG00000125207

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR (3-domain single chain)	D [auth E]	382	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.262 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.764	α = 90
b = 83.703	β = 99.6
c = 115.373	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Karuppiah, V.

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Funding Organization	Location	Grant Number
Other private	United Kingdom	--

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release