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- EMDB-2867: Structure of the helical Measles virus nucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2867
TitleStructure of the helical Measles virus nucleocapsid
Map dataReconstruction of trypsin digested Measles virus nucleocapsid
Sample
  • Sample: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
  • Protein or peptide: Nucleoprotein
KeywordsMeasles virus Nucleocapsid / Transcription and Replication template
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesMeasles virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGutsche I / Desfosses A / Effantin G / Ling WL / Haupt M / Ruigrok RWH / Sachse C / Schoehn G
CitationJournal: Science / Year: 2015
Title: Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid.
Authors: Irina Gutsche / Ambroise Desfosses / Grégory Effantin / Wai Li Ling / Melina Haupt / Rob W H Ruigrok / Carsten Sachse / Guy Schoehn /
Abstract: Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the ...Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design.
History
DepositionJan 27, 2015-
Header (metadata) releaseApr 1, 2015-
Map releaseApr 29, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4uft
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4uft
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4uft
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2867-ima...

Downloads & links

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Map

FileDownload / File: emd_2867.map.gz / Format: CCP4 / Size: 41.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of trypsin digested Measles virus nucleocapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 250 pix.
= 296.5 Å		1.19 Å/pix.
x 210 pix.
= 249.06 Å		1.19 Å/pix.
x 210 pix.
= 249.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.186 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.13157797 - 5.22336817
Average (Standard dev.)0.04398164 (±0.70481217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-105-105-125
Dimensions210210250
Spacing210210250
CellA: 249.06 Å / B: 249.06 Å / C: 296.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1861.1861.186
M x/y/z210210250
origin x/y/z0.0000.0000.000
length x/y/z249.060249.060296.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-105-105-125
NC/NR/NS210210250
D min/max/mean-3.1325.2230.044

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Supplemental data

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Sample components

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Entire : Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)

EntireName: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
Components
  • Sample: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
  • Protein or peptide: Nucleoprotein

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Supramolecule #1000: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)

SupramoleculeName: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 1

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Details: Nucleoprotein was partially digested with trypsin / Oligomeric state: Helical / Recombinant expression: Yes
Source (natural)Organism: Measles virus / Strain: Halle / synonym: Measles
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf21

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5 / Details: in 20 mM TriHCl pH 7.5, 150 mM NaCl
GridDetails: glow-discharged quantifoil grids 400 mesh 1.2/1.3
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Method: sample was applied to glow-discharged quantifoil grids 400 mesh 1.2/1.3, excess solution was blotted during 2 s with a Vitrobot Mark IV (FEI) and the grid frozen in liquid ethane

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Electron microscopy

MicroscopeFEI POLARA 300
DetailsSpecial care was taken to perform a coma-free alignment of the microscope
DateJul 1, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0008 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsFinal reconstruction obtained with SPRING
CTF correctionDetails: Each Particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.015 Å
Applied symmetry - Helical parameters - Δ&Phi: 29.173 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: SPRING / Number images used: 228165

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Atomic model buiding 1

Initial modelPDB ID:

2wj8

SoftwareName: Modeller, Chimera, Phenix, Coot
DetailsSee paper supplementary information.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-4uft:
Structure of the helical Measles virus nucleocapsid

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