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- EMDB-1707: Structural Changes in a Marine Podovirus Associated with Viral Ge... -

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Basic information

Entry
Database: EMDB / ID: EMD-1707
TitleStructural Changes in a Marine Podovirus Associated with Viral Genome Release into Prochlorococcus
Map dataThis is an image of a surface rendered top-view of P-SSP7 on the host cell surface
Sample
  • Sample: P-SSP7 of Prochlorococcus
  • Virus: Prochlorococcus phage P-SSP7 (virus)
KeywordsViral infection / electron cryo-tomography
Biological speciesProchlorococcus phage P-SSP7 (virus)
Methodsubtomogram averaging / cryo EM / negative staining
AuthorsLiu X / Zhang Q / Murata K / Baker ML / Sullivan MB / Fu C / Dougherty M / Schmid MF / Osburne MS / Chisholm SW / Chiu W
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.
Authors: Xiangan Liu / Qinfen Zhang / Kazuyoshi Murata / Matthew L Baker / Matthew B Sullivan / Caroline Fu / Matthew T Dougherty / Michael F Schmid / Marcia S Osburne / Sallie W Chisholm / Wah Chiu /
Abstract: Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of ...Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6-A and 9-A resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among five of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the 'valve' density in the nozzle, an orientation difference in the tail fibers, a disordering of the C terminus of the portal protein and the disappearance of the core proteins. In addition, cryo-electron tomography of P-SSP7 infecting Prochlorococcus showed the same tail-fiber conformation as that in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release.
History
DepositionMar 4, 2010-
Header (metadata) releaseJun 16, 2010-
Map releaseJun 16, 2010-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1707.png

Downloads & links

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Map

FileDownload / File: emd_1707.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered top-view of P-SSP7 on the host cell surface
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.36 Å/pix.
x 180 pix.
= 1684.8 Å		9.36 Å/pix.
x 180 pix.
= 1684.8 Å		9.36 Å/pix.
x 180 pix.
= 1684.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.9
Minimum - Maximum-9.49457 - 13.0662
Average (Standard dev.)0.061835 (±0.931162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 1684.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.369.369.36
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z1684.8001684.8001684.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-61-61-60
NX/NY/NZ122122122
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-9.49513.0660.062

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Supplemental data

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Sample components

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Entire : P-SSP7 of Prochlorococcus

EntireName: P-SSP7 of Prochlorococcus
Components
  • Sample: P-SSP7 of Prochlorococcus
  • Virus: Prochlorococcus phage P-SSP7 (virus)

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Supramolecule #1000: P-SSP7 of Prochlorococcus

SupramoleculeName: P-SSP7 of Prochlorococcus / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Prochlorococcus phage P-SSP7

SupramoleculeName: Prochlorococcus phage P-SSP7 / type: virus / ID: 1 / Name.synonym: P-SSP7 / NCBI-ID: 268748 / Sci species name: Prochlorococcus phage P-SSP7 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: P-SSP7
Host (natural)Organism: Podoviridae / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 655 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 100 mM Tris-HCl (pH 7.5), 100 mM MgSO4, and 30 mM NaCl
StainingType: NEGATIVE
Details: Grids with sample solution were quickly frozen in liquid ethane.
GridDetails: R3.5/1 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 90 K / Instrument: LEICA EM CPC / Details: Vitrification instrument: Leica CPC / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 90 K / Max: 95 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 80 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 20000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: -62 ° / Tilt series - Axis1 - Max angle: 62 °

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD

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