9NII | pdb_00009nii

Crystal structure of citrullinated Tenascin-C restricted PB TCR

• PDB DOI: https://doi.org/10.2210/pdb9NII/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-26 Released: 2025-05-21 
• Deposition Author(s): Dao, H.T., Loh, T.J., Lim, J.J., Rossjohn, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of citrullinated Tenascin-C restricted PB TCR

Dao, H.T., Loh, T.J., Lim, J.J., Rossjohn, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 199.47 kDa 
• Atom Count: 13,573 
• Modeled Residue Count: 1,772 
• Deposited Residue Count: 1,788 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PB TCR alpha chain	A [auth G], C [auth A], E [auth C], G [auth E]	208	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
PHAROS:  P01848

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PB TCR beta chain	B [auth H], D [auth B], F [auth D], H [auth F]	239	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth C], J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.26	α = 90
b = 119.798	β = 90
c = 176.303	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Dao, H.T., Loh, T.J., Lim, J.J., Rossjohn, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release