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- EMDB-1256: Structure of a hexameric RNA packaging motor in a viral polymeras... -

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Basic information

Entry
Database: EMDB / ID: EMD-1256
TitleStructure of a hexameric RNA packaging motor in a viral polymerase complex.
Map dataBacteriophage phi8 vertex with the hexameric packaging motor P4 reconstructed within the viral core without applying any symmetry
Sample
  • Sample: Bacteriophage phi8 core
  • Virus: Pseudomonas phage phi8 (bacteriophage)
Biological speciesPseudomonas phage phi8 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsHuiskonen JT / Jaalinoja HT / Briggs JAG
CitationJournal: J Struct Biol / Year: 2007
Title: Structure of a hexameric RNA packaging motor in a viral polymerase complex.
Authors: Juha T Huiskonen / Harri T Jäälinoja / John A G Briggs / Stephen D Fuller / Sarah J Butcher /
Abstract: Packaging of the Cystovirus varphi8 genome into the polymerase complex is catalysed by the hexameric P4 packaging motor. The motor is located at the fivefold vertices of the icosahedrally symmetric ...Packaging of the Cystovirus varphi8 genome into the polymerase complex is catalysed by the hexameric P4 packaging motor. The motor is located at the fivefold vertices of the icosahedrally symmetric polymerase complex, and the symmetry mismatch between them may be critical for function. We have developed a novel image-processing approach for the analysis of symmetry-mismatched structures and applied it to cryo-electron microscopy images of P4 bound to the polymerase complex. This approach allowed us to solve the three-dimensional structure of the P4 in situ to 15-A resolution. The C-terminal face of P4 was observed to interact with the polymerase complex, supporting the current view on RNA translocation. We suggest that the symmetry mismatch between the two components may facilitate the ring opening required for RNA loading prior to its translocation.
History
DepositionAug 11, 2006-
Header (metadata) releaseAug 11, 2006-
Map releaseMay 11, 2007-
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: 1.45
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1256.gif

Downloads & links

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Map

FileDownload / File: emd_1256.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage phi8 vertex with the hexameric packaging motor P4 reconstructed within the viral core without applying any symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 100 pix.
= 280. Å		2.8 Å/pix.
x 100 pix.
= 280. Å		2.8 Å/pix.
x 100 pix.
= 280. 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: 1.48 / Movie #1: 1.45
Minimum - Maximum-5.99879 - 6.7304
Average (Standard dev.)0.000000000005031 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 280 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-60
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-5.9996.7300.000

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Supplemental data

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Sample components

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Entire : Bacteriophage phi8 core

EntireName: Bacteriophage phi8 core
Components
  • Sample: Bacteriophage phi8 core
  • Virus: Pseudomonas phage phi8 (bacteriophage)

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Supramolecule #1000: Bacteriophage phi8 core

SupramoleculeName: Bacteriophage phi8 core / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 33 MDa

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Supramolecule #1: Pseudomonas phage phi8

SupramoleculeName: Pseudomonas phage phi8 / type: virus / ID: 1 / Name.synonym: Bacteriophage phi8 / NCBI-ID: 120086 / Sci species name: Pseudomonas phage phi8 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: Bacteriophage phi8
Host (natural)Organism: Pseudomonas syringae pv. phaseolicola (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 33 MDa
Virus shellShell ID: 1 / T number (triangulation number): 1

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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

BufferpH: 7.5
Details: 10 mM potassium phosphate pH 7.5, 1 mM MgCl2, 50 mM NaCl
GridDetails: 200 mesh holey carbon coated copper grid
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: 3.3 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 66 / Bits/pixel: 12
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle, phases flipped
Final two d classificationNumber classes: 1267
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Imagic5

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