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- EMDB-5185: CryoEM Helical Reconstruction of TMV -

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Basic information

Entry
Database: EMDB / ID: EMD-5185
TitleCryoEM Helical Reconstruction of TMV
Map dataHelically symmetrized volume of Tobacco Mosaic Virus.
Sample
  • Sample: Tobacco Mosaic Virus (Vulgare)
  • Protein or peptide: Coat Protein
KeywordsTMV / helical / RNA
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein
Function and homology information
Biological speciesunidentified (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGe P / Zhou ZH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches.
Authors: Peng Ge / Z Hong Zhou /
Abstract: Helical assemblies such as filamentous viruses, flagella, and F-actin represent an important category of structures in biology. As the first discovered virus, tobacco mosaic virus (TMV) was at the ...Helical assemblies such as filamentous viruses, flagella, and F-actin represent an important category of structures in biology. As the first discovered virus, tobacco mosaic virus (TMV) was at the center of virus research. Previously, the structure of TMV was solved at atomic detail by X-ray fiber diffraction but only for its dormant or high-calcium-concentration state, not its low-calcium-concentration state, which is relevant to viral assembly and disassembly inside host cells. Here we report a helical reconstruction of TMV in its calcium-free, metastable assembling state at 3.3 Å resolution by cryo electron microscopy, revealing both protein side chains and RNA bases. An atomic model was built de novo showing marked differences from the high-calcium, dormant-state structure. Although it could be argued that there might be inaccuracies in the latter structure derived from X-ray fiber diffraction, these differences can be interpreted as conformational changes effected by calcium-driven switches, a common regulatory mechanism in plant viruses. Our comparisons of the structures of the low- and high-calcium states indicate that hydrogen bonds formed by Asp116 and Arg92 in the place of the calcium ion of the dormant (high-calcium) state might trigger allosteric changes in the RNA base-binding pockets of the coat protein. In turn, the coat protein-RNA interactions in our structure favor an adenine-X-guanine (A*G) motif over the G*A motif of the dormant state, thus offering an explanation underlying viral assembly initiation by an AAG motif.
History
DepositionApr 12, 2010-
Header (metadata) releaseDec 8, 2010-
Map releaseMay 26, 2011-
UpdateNov 21, 2012-
Current statusNov 21, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.42
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6.42
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j06
  • Surface level: 6.42
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j06
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5185_1.png

Downloads & links

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Map

FileDownload / File: emd_5185.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelically symmetrized volume of Tobacco Mosaic Virus.
Voxel sizeX=Y=Z: 0.869 Å
Density
Contour LevelBy AUTHOR: 6.42 / Movie #1: 6.42
Minimum - Maximum-13.61543655 - 26.498800280000001
Average (Standard dev.)0.22895978 (±1.47412825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 444.928 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8690.8690.869
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z444.928444.928444.928
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-13.61526.4990.229

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Supplemental data

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Sample components

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Entire : Tobacco Mosaic Virus (Vulgare)

EntireName: Tobacco Mosaic Virus (Vulgare)
Components
  • Sample: Tobacco Mosaic Virus (Vulgare)
  • Protein or peptide: Coat Protein

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Supramolecule #1000: Tobacco Mosaic Virus (Vulgare)

SupramoleculeName: Tobacco Mosaic Virus (Vulgare) / type: sample / ID: 1000 / Oligomeric state: helix / Number unique components: 1
Molecular weightTheoretical: 37.8 MDa

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Macromolecule #1: Coat Protein

MacromoleculeName: Coat Protein / type: protein_or_peptide / ID: 1 / Name.synonym: Coat Protein / Number of copies: 2160 / Oligomeric state: helix / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others) / Strain: vulgare
Molecular weightTheoretical: 17.3 MDa
SequenceGO: helical viral capsid / InterPro: Tobacco mosaic virus-like, coat protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 10mM Tris, 130mM NaCl, pH 7.4
GridDetails: Quantifoil 1.3/1.2 400 mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification instrument: FEI Vitrobot Mark IV. 2 uL sample
Method: 10 second wait time, 1-2 second blot time, 1-2 second drain time, blot force 1

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 73000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.86 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification
Legacy - Electron beam tilt params: 0
DateJun 15, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 0.869 µm / Number real images: 386 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: EMAN
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR, EMAN

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