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- EMDB-30265: Structure of hypercondensed Mumps virus nucleocapsid at 3.6 Angst... -

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Basic information

Entry
Database: EMDB / ID: EMD-30265
TitleStructure of hypercondensed Mumps virus nucleocapsid at 3.6 Angstroms resolution
Map dataStructure of hypercondensed MuV nucleocapsid filament
Sample
  • Complex: Mumps virus nucleocapsid
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleoprotein
Function and homology information
Biological speciesMumps rubulavirus
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShen Q / Shan H / Zhang N / Qin Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: To Be Published
Title: Structure of hypercondensed Mumps nucleocapsid at 3.6 Angstroms resolution
Authors: Shen Q / Shan H / Zhang N / Qin Y
History
DepositionApr 29, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateJul 21, 2021-
Current statusJul 21, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30265.png

Downloads & links

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Map

FileDownload / File: emd_30265.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of hypercondensed MuV nucleocapsid filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.057298563 - 0.10850496
Average (Standard dev.)0.00071276334 (±0.005183453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 325.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z325.000325.000325.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0570.1090.001

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Supplemental data

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Half map: Structure of hypercondensed MuV nucleocapsid filament-hyper 2

Fileemd_30265_half_map_1.map
AnnotationStructure of hypercondensed MuV nucleocapsid filament-hyper 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of hypercondensed MuV nucleocapsid filament-hyper 1

Fileemd_30265_half_map_2.map
AnnotationStructure of hypercondensed MuV nucleocapsid filament-hyper 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mumps virus nucleocapsid

EntireName: Mumps virus nucleocapsid
Components
  • Complex: Mumps virus nucleocapsid

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Supramolecule #1: Mumps virus nucleocapsid

SupramoleculeName: Mumps virus nucleocapsid / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mumps rubulavirus
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28b

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.36 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.80 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38110
Startup modelType of model: EMDB MAP
EMDB ID:

2867

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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