9NIG | pdb_00009nig

PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide

• PDB DOI: https://doi.org/10.2210/pdb9NIG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, 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: 3.20 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

PB TCR in complex with HLA-DR4 presenting citrullinated Tenascin C peptide

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 289.11 kDa 
• Atom Count: 18,764 
• Modeled Residue Count: 2,417 
• Deposited Residue Count: 2,520 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, F [auth C], K [auth H]	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01903-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B, G [auth D], L [auth I]	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt
Find proteins for A0A1V1IGJ9 (Homo sapiens) Explore A0A1V1IGJ9  Go to UniProtKB:  A0A1V1IGJ9
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PB TCR alpha chain	C [auth M], H [auth E], M [auth J]	208	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PB TCR beta chain	D [auth N], I [auth F], N [auth K]	239	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tenascin	E [auth P], J [auth G], O [auth L]	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P24821 (Homo sapiens) Explore P24821  Go to UniProtKB:  P24821
PHAROS:  P24821 GTEx:  ENSG00000041982

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P [auth O]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Q [auth V]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	R [auth C], S [auth D], U [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	T [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CIR	E [auth P], J [auth G], O [auth L]	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.928	α = 81.468
b = 88.668	β = 76.755
c = 126.07	γ = 65.448

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