8EN8 | pdb_00008en8

Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP4 epitope from 1972 influenza strain

• PDB DOI: https://doi.org/10.2210/pdb8EN8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza A virus (A/Memphis/101/1972(H3N2))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-29 Released: 2024-03-27 
• Deposition Author(s): Littler, D.R., Rossjohn, J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors

Quinones-Parra, S.M., Littler, D.R., Rossjohn, J., Kedzierska, K.

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: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 190.19 kDa 
• Atom Count: 13,859 
• Modeled Residue Count: 1,668 
• Deposited Residue Count: 1,670 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, F	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for F4NBT2 (Homo sapiens) Explore F4NBT2  Go to UniProtKB:  F4NBT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, G	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
Nucleoprotein NP4 epitope	C, H	9	Influenza A virus (A/Memphis/101/1972(H3N2))	Mutation(s): 0
UniProt
Find proteins for Q08041 (Influenza A virus (strain A/Memphis/101/1972 H3N2)) Explore Q08041  Go to UniProtKB:  Q08041

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
3180 TCR alpha chain	D, I	205	Homo sapiens	Mutation(s): 0  Gene Names: TRAV

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
3180 TCR beta chain	E, J	245	Homo sapiens	Mutation(s): 0  Gene Names: TRBV

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.249 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.77	α = 90
b = 116.686	β = 90
c = 253.184	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Littler, D.R., Rossjohn, J.

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

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description