Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 44.85 kDa 
• Atom Count: 3464 
• Modelled Residue Count: 380 
• Deposited Residue Count: 385 
• Unique protein chains: 3

4F7P

Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009H1N1 PB1 (496-505)

• PDB DOI: 10.2210/pdb4F7P/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza A virus H3N2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-16 Released: 2012-10-10 
• Deposition Author(s): Liu, J., Zhang, S., Tan, S., Yi, Y., Wu, B., Zhu, F., Wang, H., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Cross-Allele Cytotoxic T Lymphocyte Responses against 2009 Pandemic H1N1 Influenza A Virus among HLA-A24 and HLA-A3 Supertype-Positive Individuals.

Liu, J., Zhang, S., Tan, S., Yi, Y., Wu, B., Cao, B., Zhu, F., Wang, C., Wang, H., Qi, J., Gao, G.F.

(2012) J Virol 86: 13281-13294

• PubMed: 23015716 
• DOI: 10.1128/JVI.01841-12
• Primary Citation of Related Structures:  
  4F7M, 4F7P, 4F7T


• PubMed Abstract: 
  

Lack of a universal vaccine against all serotypes of influenza A viruses and recent progress on T cell-related vaccines against influenza A virus illuminate the important role of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes (CTLs) in anti-influenza virus immunity. However, the diverse HLA alleles among humans complicate virus-specific cellular immunity research, and elucidation of cross-HLA allele T cell responses to influenza virus specificity requires further detailed work. An ideal CTL epitope-based vaccine would cover a broad spectrum of epitope antigens presented by most, if not all, of the HLAs. Here, we evaluated the 2009 pandemic influenza A (H1N1) virus-specific T cell responses among the HLA-A24(+) population using a rationally designed peptide pool during the 2009 pandemic. Unexpectedly, cross-HLA allele T cell responses against the influenza A virus peptides were detected among both HLA-A11(+) and HLA-A24(+) donors. Furthermore, we found cross-responses in the entire HLA-A3 supertype population (including HLA-A11, -A31, -A33, and -A30). The cross-allele antigenic peptides within the peptide pool were identified and characterized, and the crystal structures of the major histocompatibility complex (MHC)-peptide complexes were determined. The subsequent HLA-A24-defined cross-allele peptides recognized by the HLA-A11(+) population were shown to mildly bind to the HLA-A*1101 molecule. Together with the structural models, these results partially explain the cross-allele responses. Our findings elucidate the promiscuity of the cross-allele T cell responses against influenza A viruses and are beneficial for the development of a T cell epitope-based vaccine applied in a broader population.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-24 alpha chain	A	275	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
RNA-directed RNA polymerase catalytic subunit	C	10	Influenza A virus H3N2	Mutation(s): 0  Gene Names: PB1 EC: 2.7.7.48
UniProt
Find proteins for Q9YXL6 (Influenza A virus H3N2) Explore Q9YXL6  Go to UniProtKB:  Q9YXL6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.122	α = 90
b = 64.787	β = 90.04
c = 50.229	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-16 
• Released Date: 2012-10-10 
Deposition Author(s): Liu, J., Zhang, S., Tan, S., Yi, Y., Wu, B., Zhu, F., Wang, H., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references