8WU2 | pdb_00008wu2

Crystal structure of RNA-dependent RNA polymerases from Jingmen tick virus

• PDB DOI: https://doi.org/10.2210/pdb8WU2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Amblyomma virus GXTV108
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-20 Released: 2024-02-07 
• Deposition Author(s): Liu, Z., Han, P., Peng, Q., Qi, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.278 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

Liu, Z., Peng, Q., Han, P., Kuai, L., Qi, J., Shi, Y.

(2024) Hlife 2: 18-31

• DOI: https://doi.org/10.1016/j.hlife.2023.10.006

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 144.63 kDa 
• Atom Count: 9,520 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase	A, B	620	Amblyomma virus GXTV108	Mutation(s): 0
UniProt
Find proteins for A0A4P2RZ45 (Amblyomma virus GXTV108) Explore A0A4P2RZ45  Go to UniProtKB:  A0A4P2RZ45

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SE	C [auth A]	SELENIUM ATOM Se SPVXKVOXSXTJOY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.278 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.573	α = 90
b = 61.446	β = 104.64
c = 125.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
OASIS	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Liu, Z., Han, P., Peng, Q., Qi, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81871658

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 2.0: 2024-05-01
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy
• Version 2.1: 2024-10-09
  Changes: Structure summary