9X8S | pdb_00009x8s

Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K4ac)

• PDB DOI: https://doi.org/10.2210/pdb9X8S/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Yellow fever virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-20 Released: 2025-11-26 
• Deposition Author(s): Chen, S.D.C., Kang, S.S.K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

The structure of the human GAS41 YEATS domain in complex with an acetylated YFV capsid peptide (K4ac)

Kang, S., Li, X., Chen, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.32 kDa 
• Atom Count: 4,922 
• Modeled Residue Count: 518 
• Deposited Residue Count: 546 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEATS domain-containing protein 4	A, B, C, D	133	Homo sapiens	Mutation(s): 0  Gene Names: YEATS4, GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens) Explore O95619  Go to UniProtKB:  O95619
PHAROS:  O95619 GTEx:  ENSG00000127337

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Yellow Fever Virus Capsid Protein	E, F	7	Yellow fever virus	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	E, F	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.979	α = 90
b = 80.575	β = 100.39
c = 72.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Chen, S.D.C., Kang, S.S.K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release