9EN4 | pdb_00009en4

VP8* domain of the spike protein VP4 from bovine P[3] strain of rotavirus species C

PDB DOI: https://doi.org/10.2210/pdb9EN4/pdb

Classification: VIRAL PROTEIN
Organism(s): Bovine rotavirus C
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2024-03-12 Released: 2025-08-20
Deposition Author(s): Paredes-Martinez, F., Casino, P.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN), European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.297 (Depositor), 0.295 (DCC)
R-Value Work:
0.244 (Depositor), 0.246 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Deciphering the role of histo-blood group antigens in bovine rotavirus C infection

Navarro-Lleo, N., Ramirez-Cardenas, J., Paredes-Martinez, F., Serna, S., Gozalbo-Rovira, R., Munoz-Garcia, J.C., Reichardt, N.C., Casino, P., Angulo, J., Rodriguez-Diaz, J., Buesa, J.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.03.10.642353

Macromolecule Content

Total Structure Weight: 37.61 kDa
Atom Count: 2,623
Modeled Residue Count: 329
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP8*	A, B	165	Bovine rotavirus C	Mutation(s): 0 Gene Names: VP4
UniProt
Find proteins for L0N4C6 (Bovine rotavirus C) Explore L0N4C6 Go to UniProtKB: L0N4C6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0N4C6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.297 (Depositor), 0.295 (DCC)
R-Value Work: 0.244 (Depositor), 0.246 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.489	α = 90
b = 64.37	β = 90
c = 76.937	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Paredes-Martinez, F.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2019- 110630 GB-I00
European Regional Development Fund	European Union	PID2022-141621NB-I00

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release
Version 1.1: 2025-10-01
Changes: Structure summary

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.