8EMF

Crystal structure of a HLA-B*35:01-NP6 epitope from 1977 H1N1 influenza strain

PDB DOI: https://doi.org/10.2210/pdb8EMF/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203
R-Value Work: 0.179
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 44.86 kDa
Atom Count: 3,621
Modelled Residue Count: 385
Deposited Residue Count: 385
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4NBT2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein NP6 epitope	C	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for Q09159 (Influenza A virus (strain A/Guangdong/38/1977 H3N2)) Explore Q09159 Go to UniProtKB: Q09159
Entity Groups
UniProt Group	Q09159
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203
R-Value Work: 0.179
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51	α = 90
b = 81.645	β = 90
c = 109.239	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.