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- PDB-10id: Membrane-bound, reversed VP5* trimer (rotavirus spike protein) -

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Basic information

Entry
Database: PDB / ID: 10id
TitleMembrane-bound, reversed VP5* trimer (rotavirus spike protein)
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / non-enveloped virus / virus / viral entry / tomography
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 / subtomogram averaging / cryo EM / Resolution: 9.54 Å
Authorsde Sautu, M. / Leistner, C. / Kirchhausen, T. / Jenni, S. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI163019 United States
CitationJournal: To Be Published
Title: Mechanism of membrane perforation in rotavirus cell entry
Authors: de Sautu, M. / Leistner, C. / Kirchhausen, T. / Jenni, S. / Harrison, S.C.
History
DepositionJan 21, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / 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
4: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)259,9673
Polymers259,9673
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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P12473
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Simian rotavirus A strain RRV / Type: VIRUS
Details: Subparticle reconstruction of reversed, membrane-bound VP5* trimer
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Simian rotavirus A strain RRV
Source (recombinant)Organism: Chlorocebus aethiops (grivet) / Cell: MA104
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.3
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 3.8 e/Å2 / Avg electron dose per subtomogram: 156 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1Warpvolume selection
4WarpCTF correction
12Warp3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 9.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3255 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 537 / Num. of volumes extracted: 8565
Atomic model buildingProtocol: RIGID BODY FIT
Details: Chains 2,3,4 of PDB-ID 9C1J placed without refinement.

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