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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
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: bioRxiv / Year: 2026
Title: Mechanism of membrane perforation in rotavirus cell entry.
Authors: Marilina de Sautu / Conny Leistner / Tomas Kirchhausen / Simon Jenni / Stephen C Harrison /
Abstract: Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. ...Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. Rotaviruses and other double-strand RNA (dsRNA) viruses introduce into their target cells an inner capsid particle, roughly 700 Å in diameter, that does not uncoat further but instead extrudes capped viral mRNA by virtue of RNA-dependent RNA polymerase and capping activities within it. The delivery agent is an outer protein layer of the virion. We describe here use of cryogenic electron tomography (cryo-ET) to visualize the full course of rhesus rotavirus (RRV) entry, from cell attachment and inward budding of the virion to arrival of the subviral particle in the cytosol. The cryo-tomograms and subtomogram averaging of classified subparticles have enabled us to link high-resolution structures of the virion and its components with time series from live-cell fluorescence microscopy and thus to outline the molecular mechanism of each step in the entry process, including the hitherto elusive membrane perforation step needed for transfer of the subviral particle into the cytosol.
History
DepositionJan 21, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
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Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / 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 monkey) / 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 monkey) / 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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