9SL0 | pdb_00009sl0

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV

• PDB DOI: https://doi.org/10.2210/pdb9SL0/pdb

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


• Deposited: 2025-09-02 Released: 2025-09-17 
• Deposition Author(s): Liu, Y., Gfeller, D., Guillaume, P., Larabi, A., Lau, K., Pojer, F.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Key determinants of T cell epitope recognition revealed by TCR specificity profiles

Liu, Y., Croce, G., Tadros, D., Moreno, D., Michel, A., Thierry, A.C., Genolet, R., Perez, M.A., Lani, R., Guillaume, P., Hebeisen, M., Teleman, M., Lau, K., Larabi, A., Racle, J., Speiser, D.E., Pojer, F., Dunn, S., Baumgaertner, P., Zoete, V., Harari, A., Gfeller, D.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.11.17.688817

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: 45.18 kDa 
• Atom Count: 3,397 
• Modeled Residue Count: 382 
• 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-A
UniProt
Find proteins for A5I8L1 (Homo sapiens) Explore A5I8L1  Go to UniProtKB:  A5I8L1

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
NS5	C	9	Yellow fever virus	Mutation(s): 0
UniProt
Find proteins for W8FN10 (Yellow fever virus) Explore W8FN10  Go to UniProtKB:  W8FN10

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], G [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39SL0

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.181	α = 90
b = 80.201	β = 90
c = 111.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
autoPROC	data processing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Liu, Y., Gfeller, D., Guillaume, P., Larabi, A., Lau, K., Pojer, F.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	320030-231333

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references
• Version 1.2: 2026-04-01
  Changes: Database references