9XF9 | pdb_00009xf9

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS

• PDB DOI: https://doi.org/10.2210/pdb9XF9/pdb

• Classification: HYDROLASE
• Organism(s): Kasokero virus, Mus musculus
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-10-28 Released: 2026-05-06 
• Deposition Author(s): Deng, Z., Kuang, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS

Deng, Z., Kuang, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.6 kDa 
• Atom Count: 5,892 
• Modeled Residue Count: 677 
• Deposited Residue Count: 749 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	300	Kasokero virus	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for A0A0M5KLS1 (Kasokero virus) Explore A0A0M5KLS1  Go to UniProtKB:  A0A0M5KLS1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb 2E9 Fab heavy chain	B [auth H]	230	Mus musculus	Mutation(s): 0  Gene Names: Fab heavy chain

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb 2E9 Fab light chain	C [auth L]	219	Mus musculus	Mutation(s): 0  Gene Names: Fab light chain

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EZW (Subject of Investigation/LOI)	F [auth A]	Cap-dependent endonuclease-IN-27 C23 H19 F2 N3 O4 IYONRGIGIMDOIP-VQTJNVASSA-N
MN (Subject of Investigation/LOI)	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.32	α = 90
b = 80.6	β = 93.19
c = 116.14	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Deng, Z., Kuang, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release