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

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Database: EMDB / ID: 1316
TitleHigh-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
SampleTobacco Mosaic Virus
SourceTobacco mosaic virus / virus / 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
Methodhelical reconstruction, at 4.4 Å resolution
AuthorsSachse C / Chen JZ / Coureux PD / Stroupe ME / Fandrich M / Grigorieff N
CitationJ. Mol. Biol., 2007, 371, 812-835

J. Mol. Biol., 2007, 371, 812-835 Yorodumi Papers
High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
Carsten Sachse / James Z Chen / Pierre-Damien Coureux / M Elizabeth Stroupe / Marcus Fändrich / Nikolaus Grigorieff

Validation ReportPDB-ID: 2om3

SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2007 / Header (metadata) release: Jan 22, 2007 / Map release: Jun 25, 2007 / Last update: Apr 13, 2016

Structure visualization

  • 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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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-2om3
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1316.map.gz (map file in CCP4 format, 31251 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.16 Å/pix.
= 232.6 Å
200 pix
1.16 Å/pix.
= 232.6 Å
200 pix
1.16 Å/pix.
= 232.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.163 Å
Contour Level:0.581, 2 (movie #1):
Minimum - Maximum-5.16884 - 6.75695
Average (Standard dev.)-0.0334474 (0.671369)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 232.6 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-100-100-100
D min/max/mean-5.1696.757-0.033

Supplemental data

Sample components

Entire Tobacco Mosaic Virus

EntireName: Tobacco Mosaic Virus / Number of components: 1
MassTheoretical: 37.5 MDa

Component #1: virus, Tobacco mosaic virus

VirusName: Tobacco mosaic virus / a.k.a: Virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassExperimental: 37.5 MDa
SpeciesSpecies: Tobacco mosaic virus / virus / Virus
Source (natural)Host Species: Nicotiana tabacum / plant / タバコ / / Host category: PLANTAE(HIGHER PLANTS)

Experimental details

Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED
Sample solutionSpecimen conc.: 2.5 mg/ml / Buffer solution: Phosphate (5mM EDTA) / pH: 7.4
Support filmQuantifoil grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Method: Blot for 2 seconds before plunging / Details: Vitrification instrument: self-built model

Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Nov 22, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 60190 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4500 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 6 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: SIRT - iterative algebraic reconstruction methods
Software: Spider
CTF correction: CTFFIND and CTFTILT phase-correction and amplitude-weighting of each paritcle after Grigorieff 1998
Resolution: 4.4 Å / Resolution method: 5
Details: Final map was calculated from the central 241x241x241 cube.

Atomic model buiding

Modeling #1Software: XPLOR / Refinement protocol: flexible
Target criteria: minimization of of least-square difference between observed and calculated densities
Refinement space: REAL
Details: Protocol: Torsion angle dynamics. 2TMV pdb code structure was adjusted to fit the density for residues 88-109 and refined
Input PDB model: 2OM3
Chain ID: A, R

Overall bvalue: 90
Output model

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