4MJ6

Crystal Structure of HLA-A*1101 in complex with H7-22, an influenza A(H7N9) virus epitope

• PDB DOI: https://doi.org/10.2210/pdb4MJ6/pdb

• Classification: IMMUNE SYSTEM/PEPTIDE
• Organism(s): Homo sapiens, Influenza A virus (A/chicken/Soc Trang/4/2012(H5N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-03 Released: 2014-10-08 
• Deposition Author(s): Liu, J., Tan, S., Zhao, M., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.247 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Cross-immunity Against Avian Influenza A(H7N9) Virus in the Healthy Population Is Affected by Antigenicity-Dependent Substitutions.

Liu, W.J., Tan, S., Zhao, M., Quan, C., Bi, Y., Wu, Y., Zhang, S., Zhang, H., Xiao, H., Qi, J., Yan, J., Liu, W., Yu, H., Shu, Y., Wu, G., Gao, G.F.

(2016) J Infect Dis 214: 1937-1946

• PubMed: 27738054 
• DOI: https://doi.org/10.1093/infdis/jiw471
• Primary Citation of Related Structures:  
  4MJ5, 4MJ6


• PubMed Abstract: 
  

   The emergence of infections by the novel avian influenza A(H7N9) virus has posed a threat to human health. Cross-immunity between A(H7N9) and other heterosubtypic influenza viruses affected by antigenicity-dependent substitutions needs to be investigated.

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Organizational Affiliation: 

Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 44.97 kDa 
• Atom Count: 3,262 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-11 alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

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	C	11	Influenza A virus (A/chicken/Soc Trang/4/2012(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U8  Go to UniProtKB:  Q9Q0U8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.247 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.993	α = 90
b = 65.052	β = 90
c = 109.739	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Liu, J., Tan, S., Zhao, M., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2016-12-07
  Changes: Database references, Structure summary
• Version 1.2: 2022-08-24
  Changes: Database references