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- PDB-9c1i: Rhesus rotavirus (VP5*/VP8* structure at 3.52 Angstrom resolution) -

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Basic information

Entry
Database: PDB / ID: 9c1i
TitleRhesus rotavirus (VP5*/VP8* structure at 3.52 Angstrom resolution)
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / non-enveloped virus / viral particle
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / 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 / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsJenni, S. / Herrmann, T. / De Sautu, M. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
CitationJournal: To Be Published
Title: Rotavirus structure
Authors: Jenni, S. / Herrmann, T. / De Sautu, M. / Harrison, S.C.
History
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: Outer capsid protein VP4
3: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)173,3112
Polymers173,3112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Outer capsid protein VP4 / Hemagglutinin


Mass: 86655.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Production host: Simian rotavirus A strain RRV / References: UniProt: P12473
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Simian rotavirus A strain RRV / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Simian rotavirus A strain RRV
Source (recombinant)Organism: Simian rotavirus A strain RRV
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 542965 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 91.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00356824
ELECTRON MICROSCOPYf_angle_d0.54299324
ELECTRON MICROSCOPYf_chiral_restr0.04471030
ELECTRON MICROSCOPYf_plane_restr0.00351206
ELECTRON MICROSCOPYf_dihedral_angle_d4.7047926

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