9UZA | pdb_00009uza

Crystal structure of Crimean-Congo hemorrhagic fever virus cap-snatching endonuclease

• PDB DOI: https://doi.org/10.2210/pdb9UZA/pdb

• Classification: HYDROLASE
• Organism(s): Orthonairovirus haemorrhagiae, 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: 3.05 Å
• R-Value Free: 
  0.295 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.229 (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 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 170.81 kDa 
• Atom Count: 10,709 
• Modeled Residue Count: 1,362 
• Deposited Residue Count: 1,532 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A, D [auth B]	319	Orthonairovirus haemorrhagiae	Mutation(s): 0  EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (PDB Primary Data)
UniProt
Find proteins for D5MEH7 (Orthonairovirus haemorrhagiae) Explore D5MEH7  Go to UniProtKB:  D5MEH7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb G5 Fab heavy chain	B [auth H], E [auth C]	228	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb G5 Fab light chain	C [auth L], F [auth D]	219	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.295 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.767	α = 90
b = 99.779	β = 90
c = 180.419	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