9DY8 | pdb_00009dy8

Crystal structure of HLA-B*18:01 in complex with PEMTFFSVK, an 9-mer epitope from Influenza B

• PDB DOI: https://doi.org/10.2210/pdb9DY8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Influenza B virus (B/Wisconsin/22/2017)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-13 Released: 2025-08-13 
• Deposition Author(s): Murdolo, L.D., Maddumage, J.C., Gras, S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Characterisation of an influenza B virus-derived peptide presented by HLA-B*18:01.

Murdolo, L.D., Liwei Leong, S., Maddumage, J.C., Mifsud, N.A., Chatzileontiadou, D.S.M., Grant, E.J., Gras, S.

(2025) Biochem J 482: 811-820

• PubMed: 40587260 
• DOI: https://doi.org/10.1042/BCJ20240739
• Primary Citation Related Structures: 
  9DY8


• PubMed Abstract: 
  

  The influenza B virus (IBV) can pose a significant threat to global health. Despite this, IBV is understudied compared with influenza A virus (IAV). CD8+ T cells have proven highly effective in reducing influenza disease severity. In addition, pre-existing immune responses towards IAV epitopes may provide protection against homologous IBV-derived peptides due to T cell cross-reactivity. To exploit the advantages of T cells for future vaccine developments, a better understanding of the IBV-derived peptide presentation by the highly polymorphic human leukocyte antigen (HLA) is required. We previously determined that the IAV-derived PB1177-A peptide was presented by the HLA-B*18:01 molecule and induced CD8+ T cell responses. Here, we assessed the PB1177-A IBV homologue (PB1177-B). Intracellular cytokine staining assays showed that PB1177-B was unable to activate CD8+ T cells from several HLA-B*18:01+ samples tested. We determined that the IAVand IBV-derived PB1177 adopted different stability and conformation in the cleft of HLA-B*18:01. Molecular dynamics analysis on the crystal structure showed that PB1177-B had a central flexible region with a large hydrophobic patch formed by two phenylalanine residues, not present in PB1177-A. The flexibility and the lower stability of the HLA-B*18:01-PB1177-B complex may hinder CD8+ T cell receptor binding, underpinning the lack of CD8+ T cell activation observed. This provides additional insights into the differences between IAVand IBV-specific CD8+ T cell responses.

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Organizational Affiliation: 
• Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS), Victoria, Bundoora VIC, Australia.
Department of Biochemistry and Chemistry, La Trobe University, Victoria, Bundoora VIC, Australia.
Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
Department of Biochemistry and Molecular Biology, 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: 45.34 kDa 
• Atom Count: 3,382 
• Modeled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for S6AU73 (Homo sapiens) Explore S6AU73  Go to UniProtKB:  S6AU73

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	9	Influenza B virus (B/Wisconsin/22/2017)	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for P13871 (Influenza B virus (strain B/Ann Arbor/1/1966 [cold-adapted])) Explore P13871  Go to UniProtKB:  P13871

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	I [auth A], J [auth A], K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.821	α = 90
b = 81.423	β = 90
c = 110.345	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Murdolo, L.D., Maddumage, J.C., Gras, S.

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

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release