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

---

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

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV

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

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)

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.

---

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