9UZH | pdb_00009uzh

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with L-742,001

• PDB DOI: https://doi.org/10.2210/pdb9UZH/pdb

• Classification: HYDROLASE
• Organism(s): Kasokero virus, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2025-12-31 
• Deposition Author(s): Deng, Z., Kuang, W., Tian, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Structure and function of the nairovirus cap-snatching endonuclease

Kuang, W., Tian, Z., Zhang, G., Wu, F., Li, J., Tang, J., Zhang, H., Zhuo, X., Hu, Z., Wang, M., Zhao, H., Deng, Z.

(2025) Nucleic Acids Res 

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.57 kDa 
• Atom Count: 5,797 
• Modeled Residue Count: 678 
• 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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0N8 (Subject of Investigation/LOI)	F [auth A]	(2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid C23 H24 Cl N O4 DGJZJCIAWLMRBY-ZHZULCJRSA-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: 1.95 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.35	α = 90
b = 80.34	β = 93.37
c = 116.19	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Deng, Z., Kuang, W., Tian, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release