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

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Basic information

Entry
Database: EMDB / ID: EMD-1986
TitleCryoEM reconstruction of the Marburg virus nucleocapsid.
Map dataThis is a map of the Marburg virus nucleocapsid within virions.
Sample
  • Sample: Marburg virus nucleocapsid
  • Virus: Marburg marburgvirus
KeywordsMarburg / virus / nucleocapsid / Nucleoprotein / VP24 / VP35
Biological speciesMarburg marburgvirus
Methodhelical reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsBharat TAM / Riches JD / Kolesnikova L / Welsch S / Kraehling V / Davey N / Parsy ML / Becker S / Briggs JAG
CitationJournal: PLoS Biol / Year: 2011
Title: Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells.
Authors: Tanmay A M Bharat / James D Riches / Larissa Kolesnikova / Sonja Welsch / Verena Krähling / Norman Davey / Marie-Laure Parsy / Stephan Becker / John A G Briggs /
Abstract: Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma ...Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible "Velcro-like" manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps.
History
DepositionNov 11, 2011-
Header (metadata) releaseNov 17, 2011-
Map releaseNov 17, 2011-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1986.jpg

Downloads & links

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Map

FileDownload / File: emd_1986.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the Marburg virus nucleocapsid within virions.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 90 pix.
= 360. Å		4 Å/pix.
x 150 pix.
= 600. Å		4 Å/pix.
x 150 pix.
= 600. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00124 / Movie #1: 0.00124
Minimum - Maximum-0.00187585 - 0.00387182
Average (Standard dev.)0.00040353 (±0.000906448)
SymmetrySpace group: 0
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions15015090
Spacing15015090
CellA: 600 Å / B: 600 Å / C: 360 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Sample: Marburg virus nucleocapsid
  • Virus: Marburg marburgvirus

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Supramolecule #1000: Marburg virus nucleocapsid

SupramoleculeName: Marburg virus nucleocapsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Marburg marburgvirus

SupramoleculeName: Marburg marburgvirus / type: virus / ID: 1 / Name.synonym: Marburg virus / NCBI-ID: 11269 / Sci species name: Marburg marburgvirus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Marburg virus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferDetails: PBS buffer with 4% PFA.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunge freezer / Method: Plunge freezing

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 10 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.3 mm / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.0006 µm / Nominal magnification: 37000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.3 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider, Bsoft
CTF correctionDetails: Phase flip

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Atomic model buiding 1

Initial modelPDB ID:

2wyy

SoftwareName: Chimera
DetailsProtocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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