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- EMDB-5949: Structural Studies on the Authentic Mumps Virus Nucleocapsid Show... -

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Entry
Database: EMDB / ID: EMD-5949
TitleStructural Studies on the Authentic Mumps Virus Nucleocapsid Showing Uncoiling by the Phosphoprotein
Map dataMumps virus nucleocapsid in complex with the mumps virus phosphoprotein C-terminal nucleocapsid binding domain
Sample
  • Sample: Mumps virus nucleocapsid in complex with the C-terminal nucleocapsid binding domain of the mumps virus phosphoprotein
  • Virus: Mumps virus
Keywordsmumps phosphoprotein nucleocapsid virus replication
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 virus
Methodhelical reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsCox R / Pickar A / Qiu S / Tsao J / Rodenburg CM / Dokland T / Elson A / He B / Luo M
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Structural studies on the authentic mumps virus nucleocapsid showing uncoiling by the phosphoprotein.
Authors: Robert Cox / Adrian Pickar / Shihong Qiu / Jun Tsao / Cynthia Rodenburg / Terje Dokland / Andrew Elson / Biao He / Ming Luo /
Abstract: Mumps virus (MuV) is a highly contagious pathogen, and despite extensive vaccination campaigns, outbreaks continue to occur worldwide. The virus has a negative-sense, single-stranded RNA genome that ...Mumps virus (MuV) is a highly contagious pathogen, and despite extensive vaccination campaigns, outbreaks continue to occur worldwide. The virus has a negative-sense, single-stranded RNA genome that is encapsidated by the nucleocapsid protein (N) to form the nucleocapsid (NC). NC serves as the template for both transcription and replication. In this paper we solved an 18-Å-resolution structure of the authentic MuV NC using cryo-electron microscopy. We also observed the effects of phosphoprotein (P) binding on the MuV NC structure. The N-terminal domain of P (PNTD) has been shown to bind NC and appeared to induce uncoiling of the helical NC. Additionally, we solved a 25-Å-resolution structure of the authentic MuV NC bound with the C-terminal domain of P (PCTD). The location of the encapsidated viral genomic RNA was defined by modeling crystal structures of homologous negative strand RNA virus Ns in NC. Both the N-terminal and C-terminal domains of MuV P bind NC to participate in access to the genomic RNA by the viral RNA-dependent-RNA polymerase. These results provide critical insights on the structure-function of the MuV NC and the structural alterations that occur through its interactions with P.
History
DepositionApr 17, 2014-
Header (metadata) releaseApr 29, 2015-
Map releaseApr 29, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5949.gif

Downloads & links

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Map

FileDownload / File: emd_5949.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMumps virus nucleocapsid in complex with the mumps virus phosphoprotein C-terminal nucleocapsid binding domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.29 Å/pix.
x 200 pix.
= 458. Å		2.29 Å/pix.
x 200 pix.
= 458. Å		2.29 Å/pix.
x 200 pix.
= 458. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.003
Minimum - Maximum-0.00679553 - 0.00648742
Average (Standard dev.)0.000096 (±0.00127872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 458.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.292.292.29
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z458.000458.000458.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0070.0060.000

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Supplemental data

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Sample components

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Entire : Mumps virus nucleocapsid in complex with the C-terminal nucleocap...

EntireName: Mumps virus nucleocapsid in complex with the C-terminal nucleocapsid binding domain of the mumps virus phosphoprotein
Components
  • Sample: Mumps virus nucleocapsid in complex with the C-terminal nucleocapsid binding domain of the mumps virus phosphoprotein
  • Virus: Mumps virus

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Supramolecule #1000: Mumps virus nucleocapsid in complex with the C-terminal nucleocap...

SupramoleculeName: Mumps virus nucleocapsid in complex with the C-terminal nucleocapsid binding domain of the mumps virus phosphoprotein
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Mumps virus

SupramoleculeName: Mumps virus / type: virus / ID: 1 / NCBI-ID: 11161 / Sci species name: Mumps virus / Sci species strain: Iowa / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant cell: Vero

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsLow-dose imaging
DateApr 12, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsIHRSR using SPARX/EMAN2 package
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.32 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: SPARX

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