7UC5 | pdb_00007uc5

Crystal Structure of HLA A*0301 in complex with ILRGSVAHK, a 9-mer epitope from Influenza A

• PDB DOI: https://doi.org/10.2210/pdb7UC5/pdb

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


• Deposited: 2022-03-16 Released: 2022-10-12 
• 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: 1.95 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

CD8+ T cells cross-recognise conserved influenza A and B homologous epitopes

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

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.12 kDa 
• Atom Count: 7,394 
• Modeled Residue Count: 770 
• Deposited Residue Count: 772 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A, D	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, E	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, F	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for P26079 (Influenza A virus (strain A/Swine/Iowa/1946 H1N1)) Explore P26079  Go to UniProtKB:  P26079

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.628	α = 90
b = 155.628	β = 90
c = 170.758	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
MOLREP	phasing
XDS	data processing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
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: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary