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- EMDB-5372: Structural transitions in RCNMV revealing potential mechanism of ... -

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Basic information

Entry
Database: EMDB / ID: 5372
TitleStructural transitions in RCNMV revealing potential mechanism of RNA release (EGTA map)
Keywordscryo-electron microscopy / virus / red clover necrotic mosaic virus
SampleRCNMV
SourceRed clover necrotic mosaic virus / virus / RCNMV
Map datathis is EM map of native RCNMV with EGTA
Methodsingle particle (icosahedral) reconstruction, at 9 Å resolution
AuthorsSherman MB / Guenther RH / Tama F / Sit TL / Brooks CL / Mikhailov AM / Orlova EV / Baker TS / Lommel SA
CitationJ. Virol., 2006, 80, 10395-10406

J. Virol., 2006, 80, 10395-10406 Yorodumi Papers
Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release.
Michael B Sherman / Richard H Guenther / Florence Tama / Tim L Sit / Charles L Brooks / Albert M Mikhailov / Elena V Orlova / Timothy S Baker / Steven A Lommel

DateDeposition: Dec 16, 2011 / Header (metadata) release: Dec 19, 2011 / Map release: Dec 19, 2011 / Last update: Dec 19, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF CHIMERA
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Map

Fileemd_5372.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
2 Å/pix.
= 512. Å
256 pix
2 Å/pix.
= 512. Å
256 pix
2 Å/pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:11 (by emdb), 11 (movie #1):
Minimum - Maximum-13.9856 - 56.8837
Average (Standard dev.)0.276358 (4.91867)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 512 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-13.98656.8840.276

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Supplemental data

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Sample components

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Entire RCNMV

EntireName: RCNMV / Details: monodisperse sample / Number of components: 1
MassTheoretical: 7 MDa

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Component #1: virus, Red clover necrotic mosaic virus

VirusName: Red clover necrotic mosaic virus / a.k.a: RCNMV / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 7 MDa / Experimental: 7 MDa
SpeciesSpecies: Red clover necrotic mosaic virus / virus / RCNMV
Source (natural)Host Species: Dianthus / plant / Host category: PLANTAE(HIGHER PLANTS)

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 10 mM Tris-HCl / pH: 6.5
Support film200 mesh Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Details: Vitrification instrument: cryo-plunger

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Oct 15, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 47000 X (nominal), 49523 X (calibrated) / Astigmatism: manual / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2800 nm
Specimen HolderHolder: GATAN 626 / Model: GATAN LIQUID NITROGEN / Temperature: 95 K ( 95 - 123 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 1650 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 16 / OD range: 1.5

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 4000 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: PFT / Software: PFT / CTF correction: micrograph / Resolution: 9 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: SITUS / Refinement space: REAL / Details: Protocol: NNM
Input PDB model: 2TBV

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