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- EMDB-31361: Structure of Mumps virus nucleocapsid ring -

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Basic information

Entry
Database: EMDB / ID: EMD-31361
TitleStructure of Mumps virus nucleocapsid ring
Map data
Sample
  • Complex: Mumps virus nocleocapcid
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Keywordsnucleocapcid / Mumps virus / NUCLEAR PROTEIN
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 / Mumps virus (strain Jeryl-Lynn) / Mumps orthorubulavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSu X / Shen Q
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 25, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ewq
  • Surface level: 0.0028
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ewq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31361.png

Downloads & links

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Map

FileDownload / File: emd_31361.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 650 pix.
= 344.5 Å		0.53 Å/pix.
x 650 pix.
= 344.5 Å		0.53 Å/pix.
x 650 pix.
= 344.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0015 / Movie #1: 0.0015
Minimum - Maximum-0.0054858774 - 0.010048295
Average (Standard dev.)0.000034566627 (±0.00039210243)
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
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS650650650
D min/max/mean-0.0050.0100.000

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Supplemental data

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Sample components

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Entire : Mumps virus nocleocapcid

EntireName: Mumps virus nocleocapcid
Components
  • Complex: Mumps virus nocleocapcid
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Mumps virus nocleocapcid

SupramoleculeName: Mumps virus nocleocapcid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mumps rubulavirus

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mumps virus (strain Jeryl-Lynn) / Strain: Jeryl-Lynn
Molecular weightTheoretical: 61.470008 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY ...String:
MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY SVLIQAWVMV CKCMTAYDQP AGSADRRFAK YQQQGRLEAR YMLQPEAQRL IQTAIRKSLV VRQYLTFELQ LA RRQGLLS NRYYAMVGDI GKYIENSGLT AFFLTLKYAL GTKWSPLSLA AFTGELTKLR SLMMLYRGLG EQARYLALLE APQ IMDFAP GGYPLIFSYA MGVGTVLDVQ MRNYTYARPF LNGYYFQIGV ETARRQQGTV DNRVADDLGL TPEQRTEVTQ LVDR LARGR GAGIPGGPVN PFVPPVQQQQ PAAVYEDIPA LEESDDDGDE DGGAGFQNGV QLPAVRQGGQ TDFRAQPLQD PIQAQ LFMP LYPQVSNMPN NQNHQINRIG GLEHQDLLRY NENGDSQQDA RGEHVNTFPN NPNQNAQLQV GDWDE

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mumps orthorubulavirus
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris(hydroxymethyl)aminomethane
50.0 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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Software - Name: RELION / Number images used: 390418
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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