8EO8 | pdb_00008eo8

Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP8 epitope from 2005 H1N1 influenza strain

• PDB DOI: https://doi.org/10.2210/pdb8EO8/pdb

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


• Deposited: 2022-10-02 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: 2.30 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.183 (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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 380.72 kDa 
• Atom Count: 28,288 
• Modeled Residue Count: 3,303 
• Deposited Residue Count: 3,348 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, F, K, P	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, L, Q	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 NP8 epitope	C, H, M, R	9	Influenza A virus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
3180 alpha chain	D, I, N, S	206	Homo sapiens	Mutation(s): 0  Gene Names: TRAV13-1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
3180 beta chain	E, J, O, T	246	Homo sapiens	Mutation(s): 0  Gene Names: TRBV20-1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.088	α = 90
b = 79.468	β = 95.53
c = 172.173	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: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description