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- EMDB-5448: Cryo-tomography and subtomogram averaging of the Newcastle diseas... -

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Basic information

Entry
Database: EMDB / ID: EMD-5448
TitleCryo-tomography and subtomogram averaging of the Newcastle disease virus matrix protein array
Map dataSubtomogram average of Newcastle disease virus matrix protein
Sample
  • Sample: Newcastle disease virus matrix protein array from subtomogram averaging
  • Virus: Newcastle disease virus
Keywordsvirus assembly / matrix protein / pleomorphic virus structure / paramyxovirus / viral membrane / cryo-tomography
Biological speciesNewcastle disease virus
Methodsubtomogram averaging / cryo EM / Resolution: 45.6 Å
AuthorsBattisti AJ / Meng G / Winkler DC / McGinnes LW / Plevka P / Steven AC / Morrison TG / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure and assembly of a paramyxovirus matrix protein.
Authors: Anthony J Battisti / Geng Meng / Dennis C Winkler / Lori W McGinnes / Pavel Plevka / Alasdair C Steven / Trudy G Morrison / Michael G Rossmann /
Abstract: Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and ...Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.
History
DepositionJul 14, 2012-
Header (metadata) releaseAug 1, 2012-
Map releaseAug 15, 2012-
UpdateAug 22, 2012-
Current statusAug 22, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5448.tif

Downloads & links

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Map

FileDownload / File: emd_5448.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Newcastle disease virus matrix protein
Voxel sizeX=Y=Z: 7.5 Å
Density
Contour LevelBy AUTHOR: 2.4 / Movie #1: 2.4
Minimum - Maximum-3.50328827 - 8.704774860000001
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-52-52-12
Dimensions10510525
Spacing10510525
CellA: 787.5 Å / B: 787.5 Å / C: 187.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.57.57.5
M x/y/z10510525
origin x/y/z0.0000.0000.000
length x/y/z787.500787.500187.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-52-52-12
NC/NR/NS10510525
D min/max/mean-3.5038.7050.000

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Supplemental data

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Sample components

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Entire : Newcastle disease virus matrix protein array from subtomogram ave...

EntireName: Newcastle disease virus matrix protein array from subtomogram averaging
Components
  • Sample: Newcastle disease virus matrix protein array from subtomogram averaging
  • Virus: Newcastle disease virus

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Supramolecule #1000: Newcastle disease virus matrix protein array from subtomogram ave...

SupramoleculeName: Newcastle disease virus matrix protein array from subtomogram averaging
type: sample / ID: 1000 / Oligomeric state: an array of dimers / Number unique components: 1
Molecular weightTheoretical: 76 KDa

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Supramolecule #1: Newcastle disease virus

SupramoleculeName: Newcastle disease virus / type: virus / ID: 1 / Details: Newcastle disease virus strain B1 / NCBI-ID: 11176 / Sci species name: Newcastle disease virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Gallus gallus (chicken) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 8 / Details: 0.02 M Tris, 0.12 M NaCl, 0.001 M EDTA
GridDetails: 200 mesh holey carbon copper grids (Quantifoil Micro Tools, GmbH, Germany)
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 20000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 19500
Specialist opticsEnergy filter - Name: Tridiem GIF 863 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -64.5 ° / Tilt series - Axis1 - Max angle: 64.5 °
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 19,500 times magnification
DateOct 19, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Sampling interval: 15.0 µm / Number real images: 87 / Average electron dose: 163 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 45.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Uppsala_Software_Factory
Details: Tomographic reconstruction showed an array of matrix protein subunits, which were averaged to reduce noise. Two-fold symmetry enforced for individual subunits. Membrane density masked out.
DetailsImages aligned using colloidal gold fiducial markers and reconstructed using the weighted back-projection method as implemented in EMAN. Average number of tilts used in the 3D reconstructions: 87. Average tomographic tilt angle increment: 1.5.

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Atomic model buiding 1

Initial modelPDB ID:

4g1g


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: EMfit
DetailsProtocol: Rigid body. 10 matrix protein dimers were simultaneously fitted into the matrix array density using EMfit
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumF, clash

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