9LJR | pdb_00009ljr

Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

• PDB DOI: https://doi.org/10.2210/pdb9LJR/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hepatitis C virus JFH-1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-01-15 Released: 2025-08-13 
• Deposition Author(s): Wang, D.P., Zhao, R., Hu, W.S., Li, H.N., Cao, J.M., Zhou, X., Xiang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.174 (DCC) 

Starting Model: experimental

Literature

Structural insights into the polymerase catalyzed FAD-capping of hepatitis C viral RNA

Wang, D.P., Zhao, R., Hu, W.S., Li, H.N., Cao, J.M., Zhou, X., Xiang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 64.1 kDa 
• Atom Count: 4,610 
• Modeled Residue Count: 557 
• Deposited Residue Count: 557 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	554	Hepatitis C virus JFH-1	Mutation(s): 5  EC: 2.7.7.48
UniProt
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1)) Explore Q99IB8  Go to UniProtKB:  Q99IB8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*GP*U)-3')	B [auth T]	3	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CDP	C [auth A]	CYTIDINE-5'-DIPHOSPHATE C9 H15 N3 O11 P2 ZWIADYZPOWUWEW-XVFCMESISA-N
MN	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.174 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.876	α = 90
b = 138.876	β = 90
c = 93.227	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Wang, D.P., Zhao, R., Hu, W.S., Li, H.N., Cao, J.M., Zhou, X., Xiang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32401055, 31925023, 21827810, 31861143027

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release