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- EMDB-2341: Bacteriophage phi6 procapsids with different composition of acces... -

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Basic information

Entry
Database: EMDB / ID: EMD-2341
TitleBacteriophage phi6 procapsids with different composition of accessory proteins
Map datawildtype phi6 procapsid composed of P1, P2, P4 and P7 subunits
Sample
  • Sample: Wildtype bacteriophage phi6 procapsid
  • Virus: Pseudomonas phage phi6 (bacteriophage)
KeywordsdsRNA virus / Cystoviridae / phi6 procapsid / RNA polymerase / P7 subunit / location / occupancy
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsNemecek D / Qiao J / Mindich L / Steven AC / Heymann JB
CitationJournal: J Virol / Year: 2012
Title: Packaging accessory protein P7 and polymerase P2 have mutually occluding binding sites inside the bacteriophage 6 procapsid.
Authors: Daniel Nemecek / Jian Qiao / Leonard Mindich / Alasdair C Steven / J Bernard Heymann /
Abstract: Bacteriophage 6 is a double-stranded RNA (dsRNA) virus whose genome is packaged sequentially as three single-stranded RNA (ssRNA) segments into an icosahedral procapsid which serves as a compartment ...Bacteriophage 6 is a double-stranded RNA (dsRNA) virus whose genome is packaged sequentially as three single-stranded RNA (ssRNA) segments into an icosahedral procapsid which serves as a compartment for genome replication and transcription. The procapsid shell consists of 60 copies each of P1(A) and P1(B), two nonequivalent conformers of the P1 protein. Hexamers of the packaging ATPase P4 are mounted over the 5-fold vertices, and monomers of the RNA-dependent RNA polymerase (P2) attach to the inner surface, near the 3-fold axes. A fourth protein, P7, is needed for packaging and also promotes assembly. We used cryo-electron microscopy to localize P7 by difference mapping of procapsids with different protein compositions. We found that P7 resides on the interior surface of the P1 shell and appears to be monomeric. Its binding sites are arranged around the 3-fold axes, straddling the interface between two P1(A) subunits. Thus, P7 may promote assembly by stabilizing an initiation complex. Only about 20% of the 60 P7 binding sites were occupied in our preparations. P7 density overlaps P2 density similarly mapped, implying mutual occlusion. The known structure of the 12 homolog fits snugly into the P7 density. Both termini-which have been implicated in RNA binding-are oriented toward the adjacent 5-fold vertex, the entry pathway of ssRNA segments. Thus, P7 may promote packaging either by interacting directly with incoming RNA or by modulating the structure of the translocation pore.
History
DepositionMar 27, 2013-
Header (metadata) releaseApr 10, 2013-
Map releaseApr 10, 2013-
UpdateApr 10, 2013-
Current statusApr 10, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2341.png

Downloads & links

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Map

FileDownload / File: emd_2341.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationwildtype phi6 procapsid composed of P1, P2, P4 and P7 subunits
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 400 pix.
= 652. Å		1.63 Å/pix.
x 400 pix.
= 652. Å		1.63 Å/pix.
x 400 pix.
= 652. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.6837678 - 9.26761436
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 652.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z652.000652.000652.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-5.6849.2680.000

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Supplemental data

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Sample components

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Entire : Wildtype bacteriophage phi6 procapsid

EntireName: Wildtype bacteriophage phi6 procapsid
Components
  • Sample: Wildtype bacteriophage phi6 procapsid
  • Virus: Pseudomonas phage phi6 (bacteriophage)

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Supramolecule #1000: Wildtype bacteriophage phi6 procapsid

SupramoleculeName: Wildtype bacteriophage phi6 procapsid / type: sample / ID: 1000 / Oligomeric state: icosahedral shell with acessory proteins / Number unique components: 1
Molecular weightTheoretical: 12.6 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: No / Virus empty: Yes / Syn species name: bacteriophage phi6
Host (natural)Organism: Pseudomonas syringae (bacteria) / synonym: BACTERIA(EUBACTERIA)
Host systemOrganism: Escherichia coli (E. coli) / Recombinant strain: phi6 / Recombinant cell: JM109 / Recombinant plasmid: pLM687
Molecular weightTheoretical: 12.6 MDa
Virus shellShell ID: 1 / Diameter: 450 Å / T number (triangulation number): 2

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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

Concentration10 mg/mL
BufferpH: 8 / Details: 10mM Tris, 5mM MgCl2
GridDetails: Q-foil 2/2/300 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2s before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateFeb 20, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 112 / Average electron dose: 15 e/Å2 / Details: scanning at 4000 dpi / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.05 µm / Nominal defocus min: 0.65 µm / Nominal magnification: 38000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected manually, CTF was estimated from whole micrographs
CTF correctionDetails: CTF was determined from whole micrographs
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: Bsoft / Number images used: 6839

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