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- EMDB-1986: CryoEM reconstruction of the Marburg virus nucleocapsid. -

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Basic information

Entry
Database: EMDB / ID: 1986
TitleCryoEM reconstruction of the Marburg virus nucleocapsid.
KeywordsMarburg / virus / nucleocapsid / Nucleoprotein / VP24 / VP35
SampleMarburg virus nucleocapsid
SourceMarburg marburgvirus / virus / Marburg virus
Map dataThis is a map of the Marburg virus nucleocapsid within virions.
Methodhelical reconstruction, at 25 A resolution
AuthorsBharat TAM / Riches JD / Kolesnikova L / Welsch S / Kraehling V / Davey N / Parsy ML / Becker S / Briggs JAG
CitationPLoS Biol., 2011, 9, e1001196-e1001196

PLoS Biol., 2011, 9, e1001196-e1001196 StrPapers
Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells.
Tanmay A M Bharat / James D Riches / Larissa Kolesnikova / Sonja Welsch / Verena Krähling / Norman Davey / Marie-Laure Parsy / Stephan Becker / John A G Briggs

DateDeposition: Nov 11, 2011 / Header (metadata) release: Nov 17, 2011 / Map release: Nov 17, 2011 / Last update: Nov 11, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00124
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.00124
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1986.map.gz (map file in CCP4 format, 7912 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
4 A/pix
= 360. A
150 pix
4 A/pix
= 600. A
150 pix
4 A/pix
= 600. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4 A
Density
Contour Level:0.00124 (by author), 0.00124 (movie #1):
Minimum - Maximum-0.00187585 - 0.00387182
Average (Standard dev.)0.00040353 (0.000906448)
Details

EMDB XML:

Space Group Number0
Map Geometry
Axis orderXYZ
Dimensions15015090
Origin000
Limit14914989
Spacing15015090
CellA: 600 A / B: 600 A / C: 360 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z444
M x/y/z15015090
origin x/y/z-0.000-0.000-0.000
length x/y/z600.000600.000360.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS15015090
D min/max/mean-0.0020.0040.000

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Supplemental data

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Sample components

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Entire Marburg virus nucleocapsid

EntireName: Marburg virus nucleocapsid / Number of components: 1

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Component #1: virus, Marburg marburgvirus

VirusName: Marburg marburgvirus / a.k.a: Marburg virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Marburg marburgvirus / virus / Marburg virus
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED / Delta z: 5 A / Delta phi: 24.3 deg.
Sample solutionBuffer solution: PBS buffer with 4% PFA.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: Plunge freezing / Details: Vitrification instrument: Plunge freezer

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM120T
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000 X (nominal) / Cs: 6.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.6 - 4 nm
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: real-space helical / Software: Spider, Bsoft / CTF correction: Phase flip / Resolution: 25 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections.
Input PDB model: 2WYY

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