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- EMDB-1316: High-resolution electron microscopy of helical specimens: a fresh... -

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Basic information

Entry
Database: EMDB / ID: EMD-1316
TitleHigh-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
Map dataA 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom
Sample
  • Sample: Tobacco Mosaic Virus
  • Virus: Tobacco mosaic virus
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesTobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSachse C / Chen JZ / Coureux PD / Stroupe ME / Fandrich M / Grigorieff N
CitationJournal: J Mol Biol / Year: 2007
Title: High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
Authors: Carsten Sachse / James Z Chen / Pierre-Damien Coureux / M Elizabeth Stroupe / Marcus Fändrich / Nikolaus Grigorieff /
Abstract: The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be ...The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.
History
DepositionJan 22, 2007-
Header (metadata) releaseJan 22, 2007-
Map releaseJun 25, 2007-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing 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 cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1316.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA 69 Angstrom section of the virus. The complete virus contains contains approximately 44 repeats of this 69 Angstrom section. The section contains 49 asymmetric units of the helical virus.Cube of 241 x 241 x 241 Angstrom
Voxel sizeX=Y=Z: 1.163 Å
Density
Contour Level1: 0.581 / Movie #1: 2
Minimum - Maximum-5.16884 - 6.75695
Average (Standard dev.)-0.0334474 (±0.671369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 232.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1631.1631.163
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z232.600232.600232.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-5.1696.757-0.033

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Supplemental data

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Sample components

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Entire : Tobacco Mosaic Virus

EntireName: Tobacco Mosaic Virus
Components
  • Sample: Tobacco Mosaic Virus
  • Virus: Tobacco mosaic virus

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Supramolecule #1000: Tobacco Mosaic Virus

SupramoleculeName: Tobacco Mosaic Virus / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 37.5 MDa

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Supramolecule #1: Tobacco mosaic virus

SupramoleculeName: Tobacco mosaic virus / type: virus / ID: 1 / Name.synonym: Virus / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Virus
Host (natural)Organism: Nicotiana tabacum (common tobacco) / synonym: PLANTAE(HIGHER PLANTS)
Molecular weightExperimental: 37.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4 / Details: Phosphate (5mM EDTA)
GridDetails: Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self-built model / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DateNov 22, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 6 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: OTHER / Software - Name: Spider
Details: Final map was calculated from the central 241x241x241 cube.

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Atomic model buiding 1

Initial modelPDB ID:

Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: R
SoftwareName: XPLOR
DetailsProtocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 90
Target criteria: minimization of of least-square difference between observed and calculated densities
Output model

PDB-2om3:
High-resolution cryo-EM structure of Tobacco Mosaic Virus

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