Biological Assembly 1  

 3D View: Structure | Electron Density

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: 44.87 kDa 
• Atom Count: 3510 
• Residue Count: 385 
• Unique protein chains: 3

3LKP

Crystal Structure of HLA B*3501 in complex with influenza NP418 epitope from 1972 strain

• DOI: 10.2210/pdb3LKP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-27 Released: 2010-07-07 
• Deposition Author(s): Gras, S., Kedzierski, L., Valkenburg, S.A., Liu, Y.C., Denholm, J., Richards, M., Rimmelzwaan, G.F., Doherty, P.C., Turner, S.J., Rossjohn, J., Kedzierska, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Cross-reactive CD8+ T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses.

Gras, S., Kedzierski, L., Valkenburg, S.A., Laurie, K., Liu, Y.C., Denholm, J.T., Richards, M.J., Rimmelzwaan, G.F., Kelso, A., Doherty, P.C., Turner, S.J., Rossjohn, J., Kedzierska, K.

(2010) Proc Natl Acad Sci U S A 107: 12599-12604

• PubMed: 20616031 
• DOI: 10.1073/pnas.1007270107
• Primary Citation of Related Structures:  
  3LKN, 3LKO, 3LKP, 3LKQ, 3LKR, 3LKS


• PubMed Abstract: 
  

Preexisting T-cell immunity directed at conserved viral regions promotes enhanced recovery from influenza virus infections, with there being some evidence of cross-protection directed at variable peptides. Strikingly, many of the immunogenic peptides derived from the current pandemic A(H1N1)-2009 influenza virus are representative of the catastrophic 1918 "Spanish flu" rather than more recent "seasonal" strains. We present immunological and structural analyses of cross-reactive CD8(+) T-cell-mediated immunity directed at a variable (although highly cross-reactive) immunodominant NP(418-426) peptide that binds to a large B7 family (HLA-B*3501/03/0702) found throughout human populations. Memory CD8(+) T-cell specificity was probed for 12 different NP(418) mutants that emerged over the 9 decades between the 1918 and 2009 pandemics. Although there is evidence of substantial cross-reactivity among seasonal NP(418) mutants, current memory T-cell profiles show no preexisting immunity to the 2009-NP(418) variant or the 1918-NP(418) variant. Natural infection with the A(H1N1)-2009 virus, however, elicits CD8(+) T cells specific for the 2009-NP(418) and 1918-NP(418) epitopes. This analysis points to the potential importance of cross-reactive T-cell populations that cover the possible spectrum of T-cell variants and suggests that the identification of key residues/motifs that elicit cross-reactive T-cell sets could facilitate the evolution of immunization protocols that provide a measure of protection against unpredicted pandemic influenza viruses. Thus, it is worth exploring the potential of vaccines that incorporate peptide variants with a proven potential for broader immunogenicity, especially to those that are not recognized by the current memory T-cell pool generated by exposure to influenza variants that cause successive seasonal epidemics.

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Organizational Affiliation: 

Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-35 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889 GTEx  ENSG00000234745

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
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NP418 epitope from 1972 influenza strain	C	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.12	α = 90
b = 82.02	β = 90
c = 110.43	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Bue	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-27 
• Released Date: 2010-07-07 
Deposition Author(s): Gras, S., Kedzierski, L., Valkenburg, S.A., Liu, Y.C., Denholm, J., Richards, M., Rimmelzwaan, G.F., Doherty, P.C., Turner, S.J., Rossjohn, J., Kedzierska, K.

Revision History 

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance