Biological Assembly 1  

 3D View: Structure | 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: 44.48 kDa 
• Atom Count: 3559 
• Modelled Residue Count: 382 
• Deposited Residue Count: 382 
• Unique protein chains: 3

4NT6

HLA-C*0801 Crystal Structure

• DOI: 10.2210/pdb4NT6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza A virus (A/Boston/115JC/2009(H1N1))
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-01 Released: 2014-07-23 
• Deposition Author(s): Liu, J.X., Toh, X.Y., Ren, E.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.229 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

The immunodominant Influenza A virus M1<58-66> CTL epitope exhibits degenerate class I MHC restriction in humans

Choo, J.A., Liu, J.X., Toh, X.Y., Grotenbreg, G.M., Ren, E.C.

(2014) J Virol 

• PubMed: 24990997 
• DOI: 10.1128/JVI.00855-14
• Primary Citation of Related Structures:  
  4NT6


• PubMed Abstract: 
  

Cytotoxic T lymphocytes recognizing conserved peptide epitopes are crucial for protection against influenza A virus (IAV) infection. The CD8 T cell response against the M158-66 (GILGFVFTL) matrix protein epitope is immunodominant when restricted by HLA-A*02, a major histocompatibility complex (MHC) molecule expressed by approximately half of the human population. Here we report that the GILGFVFTL peptide is restricted by multiple HLA-C*08 alleles as well. We observed that M158-66 was able to elicit cytotoxic T lymphocyte (CTL) responses in both HLA-A*02- and HLA-C*08-positive individuals and that GILGFVFTL-specific CTLs in individuals expressing both restriction elements were distinct and not cross-reactive. The crystal structure of GILGFVFTL-HLA-C*08:01 was solved at 1.84 Å, and comparison with the known GILGFVFTL-HLA-A*02:01 structure revealed that the antigen bound both complexes in near-identical conformations, accommodated by binding pockets shaped from shared as well as unique residues. This discovery of degenerate peptide presentation by both HLA-A and HLA-C allelic variants eliciting unique CTL responses to IAV infection contributes fundamental knowledge with important implications for vaccine development strategies.

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Organizational Affiliation: 

Department of Microbiology, National University of Singapore, Singapore Singapore Immunology Network, A*STAR, Singapore [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, Cw-8 alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-C, HLAC
UniProt & NIH Common Fund Data Resources
Find proteins for P10321 (Homo sapiens) Explore P10321  Go to UniProtKB:  P10321
PHAROS:  P10321 GTEx:  ENSG00000204525

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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
Matrix protein 1	C	9	Influenza A virus (A/Boston/115JC/2009(H1N1))	Mutation(s): 0  Gene Names: M1
UniProt
Find proteins for D9J353 (Influenza A virus) Explore D9J353  Go to UniProtKB:  D9J353

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.229 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.401	α = 90
b = 75.687	β = 120.29
c = 61.88	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-01 
• Released Date: 2014-07-23 
Deposition Author(s): Liu, J.X., Toh, X.Y., Ren, E.C.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release