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- EMDB-1207: Structure of the bacteriophage phi6 nucleocapsid suggests a mecha... -

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Basic information

Entry
Database: EMDB / ID: EMD-1207
TitleStructure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
Map dataReconstruction of phi6 empty nucleocapsid
Sample
  • Sample: Bacteriophage phi6 nucleocapsid
  • Virus: Pseudomonas phage phi6 (bacteriophage)
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsHuiskonen JT / de Haas F / Bubeck D / Bamford DH / Fuller SD / Butcher SJ
CitationJournal: Structure / Year: 2006
Title: Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
Authors: Juha T Huiskonen / Felix de Haas / Doryen Bubeck / Dennis H Bamford / Stephen D Fuller / Sarah J Butcher /
Abstract: Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to ...Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to expansion of the polymerase complex, minus and plus strand RNA synthesis, and assembly of the nucleocapsid. The phi6 in vitro assembly and packaging system is a valuable model for dsRNA virus replication. The structure of the nucleocapsid at 7.5 A resolution presented here reveals the secondary structure of the two major capsid proteins. Asymmetric P1 dimers organize as an inner T = 1 shell, and P8 trimers organize as an outer T = 13 laevo shell. The organization of the P1 molecules in the unexpanded and expanded polymerase complex suggests that the expansion is accomplished by rigid body movements of the P1 monomers. This leads to exposure of new potential RNA binding surfaces to control the sequential packaging of the genome segments.
History
DepositionMar 29, 2006-
Header (metadata) releaseMar 30, 2006-
Map releaseJun 14, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1421
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1421
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1207.gif

Downloads & links

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Map

FileDownload / File: emd_1207.map.gz / Format: CCP4 / Size: 39.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of phi6 empty nucleocapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 219 pix.
= 613.2 Å		2.8 Å/pix.
x 219 pix.
= 613.2 Å		2.8 Å/pix.
x 219 pix.
= 613.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2130.0 / Movie #1: 1421
Minimum - Maximum-2191.619999999999891 - 4825.579999999999927
Average (Standard dev.)54.487699999999997 (±896.19500000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-109-109-109
Dimensions219219219
Spacing219219219
CellA=B=C: 613.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z219219219
origin x/y/z0.0000.0000.000
length x/y/z613.200613.200613.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-109-109-109
NC/NR/NS219219219
D min/max/mean-2191.6204825.57754.488

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Supplemental data

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Sample components

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Entire : Bacteriophage phi6 nucleocapsid

EntireName: Bacteriophage phi6 nucleocapsid
Components
  • Sample: Bacteriophage phi6 nucleocapsid
  • Virus: Pseudomonas phage phi6 (bacteriophage)

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Supramolecule #1000: Bacteriophage phi6 nucleocapsid

SupramoleculeName: Bacteriophage phi6 nucleocapsid / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 22 MDa

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Supramolecule #1: Pseudomonas phage phi6

SupramoleculeName: Pseudomonas phage phi6 / type: virus / ID: 1 / Name.synonym: Bacteriophage phi6 / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: Bacteriophage phi6
Host (natural)Organism: Pseudomonas syringae pv phaesolicola HB10Y / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: PC shell / Diameter: 485 Å / T number (triangulation number): 1
Virus shellShell ID: 2 / Name: NC shell / Diameter: 555 Å / T number (triangulation number): 13

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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

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: OTHER
TemperatureAverage: 93 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 37 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle, full CTF correction
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: P3DR
Details: The map was calculated from empty particles lacking the genome
Number images used: 1163

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