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- EMDB-1206: Structure of the bacteriophage phi6 nucleocapsid suggests a mecha... -

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Basic information

Entry
Database: EMDB / ID: EMD-1206
TitleStructure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging.
Map dataReconstruction of phi6 nucleocapsid to 7.5-A resolution
Sample
  • Sample: Bacteriophage phi6 nucleocapsid
  • Virus: Pseudomonas phage phi6 (bacteriophage)
Function / homology: / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 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 29, 2006-
Map releaseJun 14, 2006-
UpdateAug 28, 2013-
Current statusAug 28, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1400
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1400
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4btq
  • Surface level: 1400
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4btq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1206.gif

emd_1206_fsc...

Downloads & links

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Map

FileDownload / File: emd_1206.map.gz / Format: CCP4 / Size: 278 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of phi6 nucleocapsid to 7.5-A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 421 pix.
= 589.4 Å		1.4 Å/pix.
x 421 pix.
= 589.4 Å		1.4 Å/pix.
x 421 pix.
= 589.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1800.0 / Movie #1: 1400
Minimum - Maximum-2373.0 - 4406.0
Average (Standard dev.)108.316999999999993 (±931.765999999999963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions421421421
Spacing421421421
CellA=B=C: 589.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z421421421
origin x/y/z0.0000.0000.000
length x/y/z589.400589.400589.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-210-210-210
NC/NR/NS421421421
D min/max/mean-2373.0004406.000108.317

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Supplemental data

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Segmentation: Alpha subunit

AnnotationAlpha subunit
Fileemd_1206_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Segmentation: Beta subunit

AnnotationBeta subunit
Fileemd_1206_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: Q subunit

AnnotationQ subunit
Fileemd_1206_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: R subunit

AnnotationR subunit
Fileemd_1206_msk_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: S subunit

AnnotationS subunit
Fileemd_1206_msk_5.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Segmentation: T subunit

AnnotationT subunit
Fileemd_1206_msk_6.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: tc B

Annotationtc_B
Fileemd_1206_msk_7.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Others

Details[MASKnames]
emd_1206_msk_1.map > phi6nc_210_tc_B_mask.map
emd_1206_msk_2.map > phi6nc_421_A_mask.map
emd_1206_msk_3.map > phi6nc_421_B_mask.map
emd_1206_msk_4.map > phi6nc_421_Q_mask.map
emd_1206_msk_5.map > phi6nc_421_R_mask.map
emd_1206_msk_6.map > phi6nc_421_S_mask.map
emd_1206_msk_7.map > phi6nc_421_T_mask.ma
Image

File: emd_1206_fsc.jpg

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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
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 52 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: OTHER
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: 7.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: P3DR / Number images used: 10463

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