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- EMDB-1571: VP7 recoated rotavirus DLP -

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Basic information

Entry
Database: EMDB / ID: EMD-1571
TitleVP7 recoated rotavirus DLP
Map dataOne quadrant of the 7RP capsid.
Sample
  • Sample: VP7 recoated rotavirus DLP
  • Virus: Rotavirus
Keywordsrotavirus / capsid / VP7 / VP6 / VP2
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Inner capsid protein VP2 / Inner capsid protein VP2 / Intermediate capsid protein VP6 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesRotavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsChen JZ / Settembre EC / Aoki ST / Zhang X / Bellamy AR / Dormitzer PR / Harrison SC / Grigorieff N
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.
Authors: James Z Chen / Ethan C Settembre / Scott T Aoki / Xing Zhang / A Richard Bellamy / Philip R Dormitzer / Stephen C Harrison / Nikolaus Grigorieff /
Abstract: Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle ...Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.
History
DepositionMar 31, 2009-
Header (metadata) releaseApr 7, 2009-
Map releaseMay 18, 2009-
UpdateFeb 27, 2013-
Current statusFeb 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3gzt, PDB-3gzu
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3gzt
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3gzu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

7RP_icon.tif

Downloads & links

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Map

FileDownload / File: emd_1571.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOne quadrant of the 7RP capsid.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 800 pix.
= 986.4 Å		1.23 Å/pix.
x 800 pix.
= 986.4 Å		1.23 Å/pix.
x 800 pix.
= 986.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.233 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-3.26322436 - 7.17868042
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 986.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2331.2331.233
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z986.400986.400986.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-3.2637.179-0.000

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Supplemental data

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Sample components

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Entire : VP7 recoated rotavirus DLP

EntireName: VP7 recoated rotavirus DLP
Components
  • Sample: VP7 recoated rotavirus DLP
  • Virus: Rotavirus

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Supramolecule #1000: VP7 recoated rotavirus DLP

SupramoleculeName: VP7 recoated rotavirus DLP / type: sample / ID: 1000 / Oligomeric state: Icosahedral virus capsid / Number unique components: 1
Molecular weightExperimental: 60 MDa / Theoretical: 60 MDa / Method: Sum of all components

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Supramolecule #1: Rotavirus

SupramoleculeName: Rotavirus / type: virus / ID: 1 / Name.synonym: Rotavirus / Details: Inner-layer VP2, mid-layer VP6, outer-layer VP7 / NCBI-ID: 10912 / Sci species name: Rotavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Rotavirus
Host (natural)Organism: Bos taurus (cattle) / synonym: VERTEBRATES
Molecular weightExperimental: 60 MDa / Theoretical: 60 MDa
Virus shellShell ID: 1 / Name: VP2 VP6 VP7 / Diameter: 1000 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

Concentration5.0 mg/mL
BufferpH: 8 / Details: 20mM Tris-HCl, 50mM NaCl, 2mM CaCl2
GridDetails: C-falt grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunger / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
DateDec 1, 2007
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 7 µm / Number real images: 148 / Average electron dose: 25 e/Å2 / Od range: 1.2 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using SIGNATURE, the density map was reconstructed and refined using FREALIGN.
CTF correctionDetails: Individual particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 3780

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