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- EMDB-1663: CryoEM Model of the Vesicular Stomatitis Virus -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-1663
TitleCryoEM Model of the Vesicular Stomatitis Virus
Map dataThis is one octant of the volume of the top view of the VSV virion trunk.
Sample
  • Sample: VSV (Indiana)
  • Virus: Vesicular stomatitis virus
KeywordsNSRV / VSV / CryoEM / RNA / helix
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesVesicular stomatitis virus
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 10.6 Å
AuthorsGe P / Tsao J / Green TJ / Luo M / Zhou ZH
CitationJournal: Science / Year: 2010
Title: Cryo-EM model of the bullet-shaped vesicular stomatitis virus.
Authors: Peng Ge / Jun Tsao / Stan Schein / Todd J Green / Ming Luo / Z Hong Zhou /
Abstract: Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each ...Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer.
History
DepositionNov 18, 2009-
Header (metadata) releaseJan 26, 2010-
Map releaseMar 10, 2010-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Fig1.b.down....

Downloads & links

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Map

FileDownload / File: emd_1663.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is one octant of the volume of the top view of the VSV virion trunk.
Voxel sizeX=Y=Z: 1.532 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-6.59838 - 5.99716
Average (Standard dev.)0.00130372 (±0.998576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 490.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5321.5321.532
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z490.240490.240490.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-147
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-6.5985.9970.001

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Supplemental data

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Segmentation: This is 5 consequetive N's in the nucleocapsid

AnnotationThis is 5 consequetive N's in the nucleocapsid
Fileemd_1663_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: This is 2N with 5M in closest neighborhood of a central M-hub domain

AnnotationThis is 2N with 5M in closest neighborhood of a central M-hub domain
Fileemd_1663_msk_2.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 : VSV (Indiana)

EntireName: VSV (Indiana)
Components
  • Sample: VSV (Indiana)
  • Virus: Vesicular stomatitis virus

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Supramolecule #1000: VSV (Indiana)

SupramoleculeName: VSV (Indiana) / type: sample / ID: 1000 / Oligomeric state: Mature virion / Number unique components: 1

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Supramolecule #1: Vesicular stomatitis virus

SupramoleculeName: Vesicular stomatitis virus / type: virus / ID: 1 / Name.synonym: VSV
Details: Horse is the primary host species of the virus but Human is also possible.
NCBI-ID: 11276 / Sci species name: Vesicular stomatitis virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: VSV
Host (natural)Organism: Equus caballus (horse) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 100mM NaCl, 10nM Tris, 1mM EDTA
StainingType: NEGATIVE / Details: Cryo sample
GridDetails: Quantifoil 3.5/1 200 mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 50 % / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: manual plunger. Vitrification carried out in open room
Method: manual blot 1 second before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 98000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
DateJan 5, 2007
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS / Digitization - Sampling interval: 1.532 µm / Number real images: 212 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: Helicity determined and applied by IHRSR

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Atomic model buiding 1

Initial modelPDB ID:

2gic

SoftwareName: Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-2wyy:
CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS

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Atomic model buiding 2

Initial modelPDB ID:

2w2r

SoftwareName: Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-2wyy:
CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS

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