8EMI | pdb_00008emi

Crystal structure of a HLA-B*35:01-NP8 epitope from 2005 H1N1 influenza strain

• PDB DOI: https://doi.org/10.2210/pdb8EMI/pdb

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


• Deposited: 2022-09-27 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: 1.57 Å
• R-Value Free: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.97 kDa 
• Atom Count: 3,730 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 3

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-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	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	9	Influenza A virus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.869	α = 90
b = 81.528	β = 90
c = 109.259	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: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description