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- EMDB-31369: Structure of hyperdense Mumps virus nucleocapsid at 3.6 Angstroms... -

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Basic information

Entry
Database: EMDB / ID: EMD-31369
TitleStructure of hyperdense Mumps virus nucleocapsid at 3.6 Angstroms resolution
Map datamumps virus hyperdense nucleocapsid
Sample
  • Complex: Mumps virus nucleocapsid
    • Protein or peptide: mumps virus N protein
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
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: 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 26, 2021-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 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
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  • 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

Downloads & links

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Map

FileDownload / File: emd_31369.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmumps virus hyperdense nucleocapsid
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07078104 - 0.12169786
Average (Standard dev.)0.00044790874 (±0.005245735)
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
start NX/NY/NZ1229869
NX/NY/NZ377377377
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0710.1220.000

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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
    • Protein or peptide: mumps virus N protein

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Supramolecule #1: Mumps virus nucleocapsid

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

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Macromolecule #1: mumps virus N protein

MacromoleculeName: mumps virus N protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mumps rubulavirus
SequenceString: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHR VGALITLFSL PSAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR A NLTANEIA AYALLADDLP PTINNGTPYV HADVEGQPCD EIEQFLDRCY ...String:
MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHR VGALITLFSL PSAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR A NLTANEIA AYALLADDLP PTINNGTPYV HADVEGQPCD EIEQFLDRCY SVLIQAWVMV CK CMTAYDQ PAGSADRRFA KYQQQGRLEA RYMLQPEAQR LIQTAIRKSL VVRQYLTFEL QLA RRQGLL SNRYYAMVGD IGKYIENSGL TAFFLTLKYA LGTKWSPLSL AAFTGELTKL RSLM MLYRG LGEQARYLAL LEAPQIMDFA PGGYPLIFSY AMGVGTVLDV QMRNYTYARP FLNGY YFQI GVETARRQQG TVDNRVADDL GLTPEQRTEV TQLVDRLARG RGAGIPGGPV NPFVPP VQQ QQPAAVYEDI PALEESDDDG DEDGGAGFQN GVQLPAVRQG GQTDFRAQPL QDPIQAQ LF MPLYPQVSNM PNNQNHQINR IGGLEHQDLL RYNENGDSQQ DARGEHVNTF PNNPNQNA Q LQVGDWDE

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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 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

Startup modelType of model: EMDB MAP
EMDB ID:
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.8 °
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
FSC plot (resolution estimation)

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