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- EMDB-5369: Structural transitions in RCNMV revealing potential mechanism of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5369
TitleStructural transitions in RCNMV revealing potential mechanism of RNA release (native map)
Map datathis is EM map of native RCNMV
Sample
  • Sample: RCNMV
  • Virus: Red clover necrotic mosaic virus
Keywordscryo-electron microscopy / virus / red clover necrotic mosaic virus
Biological speciesRed clover necrotic mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsSherman MB / Guenther RH / Tama F / Sit TL / Brooks CL / Mikhailov AM / Orlova EV / Baker TS / Lommel SA
CitationJournal: J Virol / Year: 2006
Title: Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release.
Authors: 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 /
Abstract: The structure of Red clover necrotic mosaic virus (RCNMV), an icosahedral plant virus, was resolved to 8.5 A by cryoelectron microscopy. The virion capsid has prominent surface protrusions and ...The structure of Red clover necrotic mosaic virus (RCNMV), an icosahedral plant virus, was resolved to 8.5 A by cryoelectron microscopy. The virion capsid has prominent surface protrusions and subunits with a clearly defined shell and protruding domains. The structures of both the individual capsid protein (CP) subunits and the entire virion capsid are consistent with other species in the Tombusviridae family. Within the RCNMV capsid, there is a clearly defined inner cage formed by complexes of genomic RNA and the amino termini of CP subunits. An RCNMV virion has approximately 390 +/- 30 Ca2+ ions bound to the capsid and 420 +/- 25 Mg2+ ions thought to be in the interior of the capsid. Depletion of both Ca2+ and Mg2+ ions from RCNMV leads to significant structural changes, including (i) formation of 11- to 13-A-diameter channels that extend through the capsid and (ii) significant reorganization within the interior of the capsid. Genomic RNA within native capsids containing both Ca2+ and Mg2+ ions is extremely resistant to nucleases, but depletion of both of these cations results in nuclease sensitivity, as measured by a significant reduction in RCNMV infectivity. These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell.
History
DepositionDec 12, 2011-
Header (metadata) releaseDec 19, 2011-
Map releaseDec 19, 2011-
UpdateDec 19, 2011-
Current statusDec 19, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5369_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5369.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is EM map of native RCNMV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-15.3528 - 36.969900000000003
Average (Standard dev.)0.805978 (±7.82186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 384 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
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-15.35336.9700.806

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Supplemental data

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Sample components

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Entire : RCNMV

EntireName: RCNMV
Components
  • Sample: RCNMV
  • Virus: Red clover necrotic mosaic virus

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Supramolecule #1000: RCNMV

SupramoleculeName: RCNMV / type: sample / ID: 1000 / Details: monodisperse sample / Number unique components: 1
Molecular weightTheoretical: 7 MDa

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Supramolecule #1: Red clover necrotic mosaic virus

SupramoleculeName: Red clover necrotic mosaic virus / type: virus / ID: 1 / Name.synonym: RCNMV / NCBI-ID: 12267 / Sci species name: Red clover necrotic mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: RCNMV
Host (natural)Organism: Dianthus (plant) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightExperimental: 7 MDa / Theoretical: 7 MDa
Virus shellShell ID: 1 / Diameter: 366 Å / T number (triangulation number): 3

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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

Concentration1 mg/mL
BufferpH: 6.5 / Details: 10 mM Tris-HCl
GridDetails: 200 mesh Quantifoil
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: cryo-plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureMin: 95 K / Max: 123 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: manual / Legacy - Electron beam tilt params: 0
DateOct 15, 2003
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 2500 / Average electron dose: 20 e/Å2 / Od range: 1.5 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49523 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 47000
Sample stageSpecimen holder: GATAN 626 / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT / Number images used: 4000

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Atomic model buiding 1

Initial modelPDB ID:

2tbv

SoftwareName: SITUS
DetailsProtocol: NNM
RefinementSpace: REAL

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