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- EMDB-75186: Membrane-bound, reversed VP5* trimer (rotavirus spike protein) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75186
TitleMembrane-bound, reversed VP5* trimer (rotavirus spike protein)
Map dataM reconstruction local filtered and masked
Sample
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Outer capsid protein VP4
KeywordsRotavirus / non-enveloped virus / virus / viral entry / tomography / VIRAL PROTEIN
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
Methodsubtomogram averaging / cryo EM / Resolution: 9.54 Å
Authorsde Sautu M / Leistner C / Kirchhausen T / Jenni S / Harrison SC
Funding support United States, 3 items
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, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75186.png

Downloads & links

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Map

FileDownload / File: emd_75186.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationM reconstruction local filtered and masked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.2 Å/pix.
x 132 pix.
= 422.4 Å		3.2 Å/pix.
x 132 pix.
= 422.4 Å		3.2 Å/pix.
x 132 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0000637
Minimum - Maximum-0.0032653206 - 0.0048789866
Average (Standard dev.)-0.000008124193 (±0.00029319373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions132132132
Spacing132132132
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75186_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: M reconstruction half map 1

Fileemd_75186_half_map_1.map
AnnotationM reconstruction half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: M reconstruction half map 2

Fileemd_75186_half_map_2.map
AnnotationM reconstruction half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Simian rotavirus A strain RRV

EntireName: Simian rotavirus A strain RRV
Components
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Outer capsid protein VP4

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Supramolecule #1: Simian rotavirus A strain RRV

SupramoleculeName: Simian rotavirus A strain RRV / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Subparticle reconstruction of reversed, membrane-bound VP5* trimer
NCBI-ID: 444185 / Sci species name: Simian rotavirus A strain RRV / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 86.655586 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
SequenceString: MASLIYRQLL TNSYTVDLSD EIQEIGSTKT QNVTINLGPF AQTGYAPVNW GPGETNDSTT VEPVLDGPYQ PTTFNPPVDY WMLLAPTAA GVVVEGTNNT DRWLATILVE PNVTSETRSY TLFGTQEQIT IANASQTQWK FIDVVKTTQN GSYSQYGPLQ S TPKLYAVM ...String:
MASLIYRQLL TNSYTVDLSD EIQEIGSTKT QNVTINLGPF AQTGYAPVNW GPGETNDSTT VEPVLDGPYQ PTTFNPPVDY WMLLAPTAA GVVVEGTNNT DRWLATILVE PNVTSETRSY TLFGTQEQIT IANASQTQWK FIDVVKTTQN GSYSQYGPLQ S TPKLYAVM KHNGKIYTYN GETPNVTTKY YSTTNYDSVN MTAFCDFYII PREEESTCTE YINNGLPPIQ NTRNIVPLAL SA RNIISHR AQANEDIVVS KTSLWKEMQY NRDITIRFKF ASSIVKSGGL GYKWSEISFK PANYQYTYTR DGEEVTAHTT CSV NGMNDF NFNGGSLPTD FVISRYEVIK ENSYVYVDYW DDSQAFRNMV YVRSLAANLN SVICTGGDYS FALPVGQWPV MTGG AVSLH SAGVTLSTQF TDFVSLNSLR FRFRLTVEEP SFSITRTRVS RLYGLPAANP NNGKEYYEVA GRFSLISLVP SNDDY QTPI TNSVTVRQDL ERQLGELREE FNALSQEIAM SQLIDLALLP LDMFSMFSGI KSTIDAAKSM ATSVMKKFKK SGLANS VST LTDSLSDAAS SISRGASIRS VGSSASAWTD VSTQITDVSS SVSSISTQTS TISRRLRLKE MATQTEGMNF DDISAAV LK TKIDRSTQIS PNTLPDIVTE ASEKFIPNRA YRVINNDEVF EAGTDGRFFA YRVETFDEIP FDVQKFADLV TDSPVISA I IDFKTLKNLN DNYGISRQQA FNLLRSDPRV LREFINQDNP IIRNRIEQLI MQCRL

UniProtKB: Outer capsid protein VP4

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 3255
ExtractionNumber tomograms: 537 / Number images used: 8565 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsChains 2,3,4 of PDB-ID 9C1J placed without refinement.
RefinementProtocol: RIGID BODY FIT
Output model

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

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