9D9P | pdb_00009d9p

Crystal structure of CVB3 replication-linked RNA in complex with 3C protein

• PDB DOI: https://doi.org/10.2210/pdb9D9P/pdb
• NAKB: 9D9P

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Coxsackievirus B3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-08-21 Released: 2025-10-01 
• Deposition Author(s): Das, N.K., Koirala, D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CVB3 replication-linked RNA in complex with 3C protein

Das, N.K., Koirala, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.2 kDa 
• Atom Count: 4,871 
• Modeled Residue Count: 456 
• Deposited Residue Count: 474 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease 3C	B [auth A], C [auth B]	192	Coxsackievirus B3	Mutation(s): 1  EC: 3.4.22.28
UniProt
Find proteins for P03313 (Coxsackievirus B3 (strain Nancy)) Explore P03313  Go to UniProtKB:  P03313

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (90-MER)	A [auth R]	90	Coxsackievirus B3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.406	α = 90
b = 95.251	β = 98.63
c = 113.637	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
DIALS	data reduction
xia2	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Das, N.K., Koirala, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-2236996

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release