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- EMDB-30281: Structure of Mumps virus nuleocapcid ring -

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Basic information

Entry
Database: EMDB / ID: EMD-30281
TitleStructure of Mumps virus nuleocapcid ring
Map data
Sample
  • Complex: Mumps virus nucleocapsid
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesMumps rubulavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShen Q / Shan H / Qin Y / Su X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: Commun Biol / Year: 2021
Title: Structural plasticity of mumps virus nucleocapsids with cryo-EM structures.
Authors: Hong Shan / Xin Su / Tianhao Li / Yuqi Qin / Na Zhang / Liuyan Yang / Linsha Ma / Yun Bai / Lei Qi / Yunhui Liu / Qing-Tao Shen /
Abstract: Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a ...Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a single-stranded negative-sense RNA as its genome, which is enwrapped by viral nucleoproteins into the helical nucleocapsid. The nucleocapsid acts as a scaffold for genome condensation and as a template for RNA replication and transcription. Conformational changes in the MuV nucleocapsid are required to switch between different activities, but the underlying mechanism remains elusive due to the absence of high-resolution structures. Here, we report two MuV nucleoprotein-RNA rings with 13 and 14 protomers, one stacked-ring filament and two nucleocapsids with distinct helical pitches, in dense and hyperdense states, at near-atomic resolutions using cryo-electron microscopy. Structural analysis of these in vitro assemblies indicates that the C-terminal tail of MuV nucleoprotein likely regulates the assembly of helical nucleocapsids, and the C-terminal arm may be relevant for the transition between the dense and hyperdense states of helical nucleocapsids. Our results provide the molecular mechanism for structural plasticity among different MuV nucleocapsids and create a possible link between structural plasticity and genome condensation.
History
DepositionMay 10, 2020-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateMay 12, 2021-
Current statusMay 12, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0019
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30281.png

Downloads & links

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Map

FileDownload / File: emd_30281.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.53 Å
Density
Contour LevelBy AUTHOR: 0.0019 / Movie #1: 0.0019
Minimum - Maximum-0.0020871768 - 0.0054065725
Average (Standard dev.)4.2059775e-05 (±0.00029945685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions650650650
Spacing650650650
CellA=B=C: 344.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.530.530.53
M x/y/z650650650
origin x/y/z0.0000.0000.000
length x/y/z344.500344.500344.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS650650650
D min/max/mean-0.0020.0050.000

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Supplemental data

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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 BL21(DE3) (bacteria) / Recombinant plasmid: pET28b

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris(hydroxymethyl)aminomethane
150.0 mMNaClSodium chloridesodium 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 390418
FSC plot (resolution estimation)

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