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- EMDB-18655: Cryo-EM reconstruction of VP5*/VP8* assembly from SA11 Rotavirus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18655
TitleCryo-EM reconstruction of VP5*/VP8* assembly from SA11 Rotavirus Tripsinized Triple Layered Particle
Map data
Sample
  • Virus: Rotavirus A
    • Protein or peptide: Outer capsid protein VP4
KeywordsRotavirus / dsRNA virus / VIRUS
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 speciesRotavirus / Rotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsAsensio-Cob D / Perez-Mata C / Gomez-Blanco J / Vargas J / Rodriguez JM / Luque D
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesISCIII-AESI PI20CIII/00014 Spain
CitationJournal: bioRxiv / Year: 2025
Title: Structural determinants of rotavirus proteolytic activation.
Authors: Dunia Asensio-Cob / Carlos P Mata / Josué Gómez-Blanco / Javier Vargas / Javier M Rodríguez / Daniel Luque /
Abstract: The infectivity of rotavirus (RV), the leading cause of childhood diarrhea, hinges on the activation of viral particles through the proteolysis of the spike protein by trypsin-like proteases in the ...The infectivity of rotavirus (RV), the leading cause of childhood diarrhea, hinges on the activation of viral particles through the proteolysis of the spike protein by trypsin-like proteases in the host intestinal lumen. Despite comprehensive structural characterization of the virus particle, the structural rationale behind the necessity of trypsin digestion of the VP4 protein for infectivity remains poorly understood. In this study, using cryo-electron microscopy (cryo-EM) and advanced image processing techniques, we compared uncleaved and cleaved RV virions and found that the conformation of the non-proteolyzed spike is constrained by the position of loops that surround its structure, linking the lectin domains of the spike head to its body. The proteolysis of these loops removes this structural constraint, thereby enabling the spike to undergo the necessary conformational changes required for cell membrane penetration. Thus, these loops function as regulatory elements to ensure that the spike protein is activated precisely when and where it is needed to facilitate a successful infection.
History
DepositionOct 13, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18655.png

Downloads & links

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Map

FileDownload / File: emd_18655.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 200 pix.
= 286. Å		1.43 Å/pix.
x 200 pix.
= 286. Å		1.43 Å/pix.
x 200 pix.
= 286. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum0.0 - 16.672927999999999
Average (Standard dev.)0.08755006 (±0.829578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Rotavirus A

EntireName: Rotavirus A
Components
  • Virus: Rotavirus A
    • Protein or peptide: Outer capsid protein VP4

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Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Rotavirus SA11 Non-tripsinized spike / NCBI-ID: 28875 / Sci species name: Rotavirus A / Sci species strain: SA11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chlorocebus aethiops (grivet)
Molecular weightTheoretical: 92 MDa
Virus shellShell ID: 1 / Name: TLP / Diameter: 700.0 Å

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Macromolecule #1: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 1 / Details: Outer capsid protein VP4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus
Molecular weightTheoretical: 86.749891 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MASLIYRQLL TNSYTVDLSD EIQEIGSTKS QNVTINPGPF AQTGYAPVNW GPGEINDSTT VEPLLDGPYQ PTTFNPPVDY WMLLAPTTP GVIVEGTNNT DRWLATILIE PNVQSENRTY TIFGIQEQLT VSNTSQDQWK FIDVVKTTAN GSIGQYGSLL S SPKLYAVM ...String:
MASLIYRQLL TNSYTVDLSD EIQEIGSTKS QNVTINPGPF AQTGYAPVNW GPGEINDSTT VEPLLDGPYQ PTTFNPPVDY WMLLAPTTP GVIVEGTNNT DRWLATILIE PNVQSENRTY TIFGIQEQLT VSNTSQDQWK FIDVVKTTAN GSIGQYGSLL S SPKLYAVM KHNEKLYTYE GQTPNARTGH YSTTNYDSVN MTAFCDFYII PRSEESKCTE YINNGLPPIQ NTRNVVPLSL TA RDVIHYR AQANEDIVIS KTSLWKEMQY NRDITIRFKF ANTIIKSGGL GYKWSEISFK PANYQYTYTR DGEEVTAHTT CSV NGVNDF SFNGGSLPTD FVVSKFEVIK ENSYVYIDYW DDSQAFRNVV YVRSLAANLN SVMCTGGSYN FSLPVGQWPV LTGG AVSLH SAGVTLSTQF TDFVSLNSLR FRFRLAVEEP HFKLTRTRLD RLYGLPAADP NNGKEYYEIA GRFSLISLVP SNDDY QTPI ANSVTVRQDL ERQLGELREE FNALSQEIAM SQLIDLALLP LDMFSMFSGI KSTIDAAKSM ATNVMKKFKK SGLANS VST LTDSLSDAAS SISRGSSIRS IGSSASAWTD VSTQITDISS SVSSVSTQTS TISRRLRLKE MATQTEGMNF DDISAAV LK TKIDKSTQIS PNTIPDIVTE ASEKFIPNRA YRVINNDDVF EAGIDGKFFA YKVDTFEEIP FDVQKFADLV TDSPVISA I IDFKTLKNLN DNYGITKQQA FNLLRSDPRV LREFINQDNP IIRNRIEQLI MQCRL

UniProtKB: Outer capsid protein VP4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP
DetailsRotavirus SA11 Tripsinized spike

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2368 / Average electron dose: 39.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 58000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 28427
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

2574

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 22394
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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