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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: 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 A 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 StrPapers
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

DateDeposition: Jan 22, 2007 / Header (metadata) release: Jan 22, 2007 / Map release: Jun 25, 2007 / Last update: Jan 22, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1316.map.gz (map file in CCP4 format, 31251 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.16 A/pix
= 232.6 A
200 pix
1.16 A/pix
= 232.6 A
200 pix
1.16 A/pix
= 232.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 232.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 1
MassTheoretical: 37.5 MDa

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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)

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Experimental details

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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

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Nov 22, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / 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

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Image acquisition

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

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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 A / Resolution method: 5
Details: Final map was calculated from the central 241x241x241 cube.

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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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