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- EMDB-1060: Electron cryomicroscopy and bioinformatics suggest protein fold m... -

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Basic information

Entry
Database: EMDB / ID: EMD-1060
TitleElectron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.
Map dataThis is the 3f average map from Rice Dwarf Virus
Sample
  • Sample: Rice Dwarf Virus
  • Virus: Rice dwarf virus
Biological speciesRice dwarf virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsZhou ZH / Baker ML / Jiang W / Dougherty M / Jakana J / Dong G / Lu G / Chiu W
CitationJournal: Nat Struct Biol / Year: 2001
Title: Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.
Authors: Z H Zhou / M L Baker / W Jiang / M Dougherty / J Jakana / G Dong / G Lu / W Chiu /
Abstract: The three-dimensional structure of rice dwarf virus was determined to 6.8 A resolution by single particle electron cryomicroscopy. By integrating the structural analysis with bioinformatics, the ...The three-dimensional structure of rice dwarf virus was determined to 6.8 A resolution by single particle electron cryomicroscopy. By integrating the structural analysis with bioinformatics, the folds of the proteins in the double-shelled capsid were derived. In the outer shell protein, the uniquely orientated upper and lower domains are composed of similar secondary structure elements but have different relative orientations from that of bluetongue virus in the same Reoviridae family. Differences in both sequence and structure between these proteins may be important in defining virus-host interactions. The inner shell protein adopts a conformation similar to other members of Reoviridae, suggesting a common ancestor that has evolved to infect hosts ranging from plants to animals. Symmetry mismatch between the two shells results in nonequivalent, yet specific, interactions that contribute to the stability of this large macromolecular machine.
History
DepositionAug 11, 2003-
Header (metadata) releaseOct 21, 2003-
Map releaseApr 8, 2005-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1060.gif

Downloads & links

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Map

FileDownload / File: emd_1060.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the 3f average map from Rice Dwarf Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 140 pix.
= 229.6 Å		1.64 Å/pix.
x 279 pix.
= 457.56 Å		1.64 Å/pix.
x 279 pix.
= 457.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.38 / Movie #1: 1.5
Minimum - Maximum-8.18793 - 9.502140000000001
Average (Standard dev.)0.086981 (±1.45153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-139-139-70
Dimensions279279140
Spacing279279140
CellA: 457.56 Å / B: 457.56 Å / C: 229.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z279279140
origin x/y/z0.0000.0000.000
length x/y/z457.560457.560229.600
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-139-139-70
NC/NR/NS279279140
D min/max/mean-8.1889.5020.087

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Supplemental data

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Supplemental map: emd 1060 additional 1.map

Fileemd_1060_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1060 additional 2.map

Fileemd_1060_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1060 averaged monomer.mrc

Fileemd_1060_averaged_monomer.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1060 averaged trimer.mrc

Fileemd_1060_averaged_trimer.mrc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rice Dwarf Virus

EntireName: Rice Dwarf Virus
Components
  • Sample: Rice Dwarf Virus
  • Virus: Rice dwarf virus

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Supramolecule #1000: Rice Dwarf Virus

SupramoleculeName: Rice Dwarf Virus / type: sample / ID: 1000 / Details: Full capsid / Number unique components: 1
Molecular weightTheoretical: 50 MDa

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Supramolecule #1: Rice dwarf virus

SupramoleculeName: Rice dwarf virus / type: virus / ID: 1 / Name.synonym: rdv / NCBI-ID: 10991 / Sci species name: Rice dwarf virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: rdv
Host (natural)synonym: PLANTAE(HIGHER PLANTS)
Virus shellShell ID: 1 / Name: P3 / Diameter: 590 Å / T number (triangulation number): 1
Virus shellShell ID: 2 / Name: P8 / Diameter: 700 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 / Chamber humidity: 27 % / Chamber temperature: 111 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual

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Electron microscopy

MicroscopeJEOL 4000
TemperatureAverage: 109 K
DetailsMicroscope:JEOL 4000
DateJan 1, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 162 / Average electron dose: 13 e/Å2 / Camera length: 200 / Bits/pixel: 12
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49495 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: per micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC,IMRS / Number images used: 3261

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Atomic model buiding 1

Initial modelPDB ID:

2btv

SoftwareName: Foldhunter
DetailsFOLDHUNTER is decribed in Jiang et al , J.Mol.Biol., 308, 1033-1044 (2001). Beta sheet domain BTV VP7 blurred to 7 angstroms using the program PDB2MRC (Ludtke et at, J.Struct.Biol.,128, 82-97 (1999).
RefinementOverall B value: 100

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