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- EMDB-3184: Localized reconstruction of rotavirus VP4 spike -

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Basic information

Entry
Database: EMDB / ID: EMD-3184
TitleLocalized reconstruction of rotavirus VP4 spike
Map dataLocalized reconstruction of rotavirus VP4 spike calculated from a previously published dataset by Settembre et al. (2011)
Sample
  • Sample: Rotavirus triple-layered particle
  • Virus: Rhesus Rotavirus (RRV)
Keywordsrotavirus / VP4 / spike / triple-layered particle
Biological speciesRhesus Rotavirus (RRV)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsIlca S / Kotecha A / Sun X / Poranen MP / Stuart DI / Huiskonen JT
CitationJournal: EMBO J / Year: 2011
Title: Atomic model of an infectious rotavirus particle.
Authors: Ethan C Settembre / James Z Chen / Philip R Dormitzer / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling ...Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.
History
DepositionOct 3, 2015-
Header (metadata) releaseOct 28, 2015-
Map releaseNov 4, 2015-
UpdateNov 25, 2015-
Current statusNov 25, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3184.jpg

emd_3184.jpg

Downloads & links

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Map

FileDownload / File: emd_3184.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstruction of rotavirus VP4 spike calculated from a previously published dataset by Settembre et al. (2011)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.46 Å/pix.
x 100 pix.
= 246. Å		2.46 Å/pix.
x 100 pix.
= 246. Å		2.46 Å/pix.
x 100 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.05322818 - 0.12600207
Average (Standard dev.)0.00623467 (±0.01109883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.462.462.46
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0530.1260.006

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Supplemental data

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Segmentation: Localized reconstruction of rotavirus VP4 spike

AnnotationLocalized reconstruction of rotavirus VP4 spike
Fileemd_3184_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rotavirus triple-layered particle

EntireName: Rotavirus triple-layered particle
Components
  • Sample: Rotavirus triple-layered particle
  • Virus: Rhesus Rotavirus (RRV)

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Supramolecule #1000: Rotavirus triple-layered particle

SupramoleculeName: Rotavirus triple-layered particle / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Rhesus Rotavirus (RRV)

SupramoleculeName: Rhesus Rotavirus (RRV) / type: virus / ID: 1 / Name.synonym: Rotavirus / Sci species name: Rhesus Rotavirus (RRV) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Rotavirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 100 MDa
Virus shellShell ID: 1 / Name: Virus shell 1 / Diameter: 800 Å / T number (triangulation number): 13

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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

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
DetailsCut-plate film holders to reduce electron back-scattering
DateJan 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 110 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56770 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected from the best class averages with high VP4 occupancy
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: OTHER / Software - Name: Relion
Details: Final map was postprocessed in Relion. Inverse B-factor of 487 was applied.
Number images used: 112049
FSC plot (resolution estimation)

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