9D9O | pdb_00009d9o

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

PDB DOI: https://doi.org/10.2210/pdb9D9O/pdb
NAKB: 9D9O

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Das, N.K., Koirala, D.

To be published.

Macromolecule Content

Total Structure Weight: 54.41 kDa
Atom Count: 3,629
Modeled Residue Count: 402
Deposited Residue Count: 420
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease 3C	A, 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03313
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (36-MER)	C [auth R]	36	Coxsackievirus B3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.3	α = 90
b = 78.869	β = 90
c = 106.508	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.