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- EMDB-1622: Helical reconstruction of Respiratory Syncytial Virus N-RNA helices -

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Basic information

Entry
Database: EMDB / ID: EMD-1622
TitleHelical reconstruction of Respiratory Syncytial Virus N-RNA helices
Map dataHelical reconstruction of Respiratory Syncytial Virus N-RNA nucleocapsid-like structure. (Related to PDB entry 2wj8)
Sample
  • Sample: Respiratory Syncytial Virus Nucleoprotein-RNA
  • Protein or peptide: Nucleocapsid proteinVirus
Keywordsparamyxovirus / virus / nucleocapsid / RNP / nucleoprotein
Biological speciesRespiratory syncytial virus
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 26.0 Å
AuthorsMacLellan K / Yeo RP / Bhella D
CitationJournal: Science / Year: 2009
Title: Crystal structure of a nucleocapsid-like nucleoprotein-RNA complex of respiratory syncytial virus.
Authors: Rajiv G Tawar / Stéphane Duquerroy / Clemens Vonrhein / Paloma F Varela / Laurence Damier-Piolle / Nathalie Castagné / Kirsty MacLellan / Hugues Bedouelle / Gérard Bricogne / David Bhella ...Authors: Rajiv G Tawar / Stéphane Duquerroy / Clemens Vonrhein / Paloma F Varela / Laurence Damier-Piolle / Nathalie Castagné / Kirsty MacLellan / Hugues Bedouelle / Gérard Bricogne / David Bhella / Jean-François Eléouët / Félix A Rey /
Abstract: The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of ...The respiratory syncytial virus (RSV) is an important human pathogen, yet neither a vaccine nor effective therapies are available to treat infection. To help elucidate the replication mechanism of this RNA virus, we determined the three-dimensional (3D) crystal structure at 3.3 A resolution of a decameric, annular ribonucleoprotein complex of the RSV nucleoprotein (N) bound to RNA. This complex mimics one turn of the viral helical nucleocapsid complex, which serves as template for viral RNA synthesis. The RNA wraps around the protein ring, with seven nucleotides contacting each N subunit, alternating rows of four and three stacked bases that are exposed and buried within a protein groove, respectively. Combined with electron microscopy data, this structure provides a detailed model for the RSV nucleocapsid, in which the bases are accessible for readout by the viral polymerase. Furthermore, the nucleoprotein structure highlights possible key sites for drug targeting.
History
DepositionMay 26, 2009-
Header (metadata) releaseMay 28, 2009-
Map releaseDec 1, 2009-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 140
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 140
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1622.png

Downloads & links

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Map

FileDownload / File: emd_1622.map.gz / Format: CCP4 / Size: 16.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of Respiratory Syncytial Virus N-RNA nucleocapsid-like structure. (Related to PDB entry 2wj8)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 256 pix.
= 558.08 Å		2.18 Å/pix.
x 130 pix.
= 283.4 Å		2.18 Å/pix.
x 130 pix.
= 283.4 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: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 140.0 / Movie #1: 140
Minimum - Maximum0.0 - 551.369000000000028
Average (Standard dev.)41.552199999999999 (±99.010900000000007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130256
Spacing130130256
CellA: 283.4 Å / B: 283.4 Å / C: 558.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z130130256
origin x/y/z0.0000.0000.000
length x/y/z283.400283.400558.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130256
D min/max/mean0.000551.36941.552

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Supplemental data

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Sample components

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Entire : Respiratory Syncytial Virus Nucleoprotein-RNA

EntireName: Respiratory Syncytial Virus Nucleoprotein-RNA
Components
  • Sample: Respiratory Syncytial Virus Nucleoprotein-RNA
  • Protein or peptide: Nucleocapsid proteinVirus

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Supramolecule #1000: Respiratory Syncytial Virus Nucleoprotein-RNA

SupramoleculeName: Respiratory Syncytial Virus Nucleoprotein-RNA / type: sample / ID: 1000 / Details: Nucleoprotein was expressed in insect cells / Number unique components: 1

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Macromolecule #1: Nucleocapsid protein

MacromoleculeName: Nucleocapsid protein / type: protein_or_peptide / ID: 1 / Name.synonym: nucleoprotein / Oligomeric state: helical / Recombinant expression: Yes
Source (natural)Organism: Respiratory syncytial virus / synonym: RSV / Cell: SF21
Molecular weightTheoretical: 43 MDa
Recombinant expressionOrganism: unidentified baculovirus

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: Phosphate buffered saline
StainingType: NEGATIVE
Details: Cryo-negative staining 5 ul of protein suspension at an approximate concentration of 0.2 mg/ml was loaded onto a freshly glow-discharged Quantifoil holey carbon support film for ...Details: Cryo-negative staining 5 ul of protein suspension at an approximate concentration of 0.2 mg/ml was loaded onto a freshly glow-discharged Quantifoil holey carbon support film for approximately 10 seconds. The grid was then transferred to a droplet of 20% (w/v) ammonium molybdate solution (pH 7.4) for approximately 10 seconds, blotted for 2-3 seconds and plunged into a bath of liquid nitrogen cooled ethane slush
GridDetails: 400 mesh quantifoil
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: blot for 2 seconds, wait for 2 seconds plunge

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Electron microscopy

MicroscopeJEOL 1200EXII
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 29200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 3.4 mm / Nominal magnification: 30000
Sample stageSpecimen holder: side entry / Specimen holder model: OTHER
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected at 200k x
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 2.18 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 16

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 7 Å
Applied symmetry - Helical parameters - Δ&Phi: 36.8 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: SPIDER, HELICALS, HELICALI

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