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- PDB-9en4: VP8* domain of the spike protein VP4 from bovine P[3] strain of r... -

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Basic information

Entry
Database: PDB / ID: 9en4
TitleVP8* domain of the spike protein VP4 from bovine P[3] strain of rotavirus species C
ComponentsOuter capsid protein VP8*
KeywordsVIRAL PROTEIN / Rotavirus / spike protein / host-virus identification
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / permeabilization of host organelle membrane involved in viral entry into host cell / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesBovine rotavirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsParedes-Martinez, F. / Casino, F.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019- 110630 GB-I00 Spain
European Regional Development FundPID2022-141621NB-I00European Union
CitationJournal: Biorxiv / Year: 2025
Title: Deciphering the role of histo-blood group antigens in bovine rotavirus C infection
Authors: 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.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein VP8*
B: Outer capsid protein VP8*


Theoretical massNumber of molelcules
Total (without water)37,6112
Polymers37,6112
Non-polymers00
Water91951
1
A: Outer capsid protein VP8*


Theoretical massNumber of molelcules
Total (without water)18,8061
Polymers18,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP8*


Theoretical massNumber of molelcules
Total (without water)18,8061
Polymers18,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.489, 64.370, 76.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer capsid protein VP8*


Mass: 18805.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine rotavirus C / Strain: P[3] / Gene: VP4 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / References: UniProt: L0N4C6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.025 Å3/Da / Density % sol: 39.31292 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium Acetate 1.5 M pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→76.94 Å / Num. obs: 6504 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.365 / Rpim(I) all: 0.104 / Rrim(I) all: 0.379 / Χ2: 1 / Net I/σ(I): 7.7 / Num. measured all: 83626
Reflection shellResolution: 3→3.18 Å / % possible obs: 99.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.084 / Num. measured all: 13907 / Num. unique obs: 1033 / CC1/2: 0.873 / Rpim(I) all: 0.303 / Rrim(I) all: 1.126 / Χ2: 1.02 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.37 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.83 / SU B: 28.122 / SU ML: 0.498 / Cross valid method: THROUGHOUT / ESU R Free: 0.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29722 322 5 %RANDOM
Rwork0.24438 ---
obs0.24714 6152 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.166 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å2-0 Å2-0 Å2
2--1.7 Å2-0 Å2
3---2.57 Å2
Refinement stepCycle: 1 / Resolution: 3→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 0 51 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0112642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162364
X-RAY DIFFRACTIONr_angle_refined_deg0.5781.6283620
X-RAY DIFFRACTIONr_angle_other_deg0.2211.5575424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.61855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86110388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0270.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3623.5741314
X-RAY DIFFRACTIONr_mcbond_other0.3623.5741314
X-RAY DIFFRACTIONr_mcangle_it0.6846.4221639
X-RAY DIFFRACTIONr_mcangle_other0.6846.4221640
X-RAY DIFFRACTIONr_scbond_it0.1833.5581328
X-RAY DIFFRACTIONr_scbond_other0.1833.5591329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3846.5621982
X-RAY DIFFRACTIONr_long_range_B_refined1.74137.582877
X-RAY DIFFRACTIONr_long_range_B_other1.73837.612873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 27 -
Rwork0.35 448 -
obs--98.96 %

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