7MLE

Crystal Structure of HLA-A*03:01 in complex with VVRPSVASK, an 9-mer epitope from Influenza B virus

• PDB DOI: https://doi.org/10.2210/pdb7MLE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza B virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-28 Released: 2022-04-06 
• Deposition Author(s): Gras, S., Nguyen, A.T., Szeto, C.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Literature

Homologous peptides derived from influenza A, B and C viruses induce variable CD8 + T cell responses with cross-reactive potential.

Nguyen, A.T., Lau, H.M.P., Sloane, H., Jayasinghe, D., Mifsud, N.A., Chatzileontiadou, D.S., Grant, E.J., Szeto, C., Gras, S.

(2022) Clin Transl Immunology 11: e1422-e1422

• PubMed: 36275878 
• DOI: https://doi.org/10.1002/cti2.1422
• Primary Citation of Related Structures:  
  7MLE


• PubMed Abstract: 
  

  Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally, infecting humans and causing widespread morbidity and mortality. Here, we investigate the T cell response towards an immunodominant IAV epitope, NP _265-273, and its IBV and ICV homologues, presented by HLA-A*03:01 molecule expressed in ~ 4% of the global population (~ 300 million people).

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute Monash University Clayton VIC Australia.

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: 45.07 kDa 
• Atom Count: 3,508 
• Modelled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A	277	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 peptide	C	9	Influenza B virus	Mutation(s): 0
UniProt
Find proteins for P13884 (Influenza B virus (strain B/Ann Arbor/1/1966 [cold-adapted])) Explore P13884  Go to UniProtKB:  P13884

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.265	α = 90
b = 155.265	β = 90
c = 85.331	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Gras, S., Nguyen, A.T., Szeto, C.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1159272

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description