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- EMDB-31370: Structure of ring-stacked Mumps virus nucleocapsid filament -

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Basic information

Entry
Database: EMDB / ID: EMD-31370
TitleStructure of ring-stacked Mumps virus nucleocapsid filament
Map dataring-stacked MuV 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31370.png

Downloads & links

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Map

FileDownload / File: emd_31370.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationring-stacked MuV nucleocapsid
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-0.05851113 - 0.09396639
Average (Standard dev.)0.00056654157 (±0.0046004853)
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-0.0590.0940.001

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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 BL21(DE3) (bacteria) / 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
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 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 79901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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