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- EMDB-1714: Asymmetric structure of the empty Prochlorococcus Cyanophage P-SSP7 -

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Basic information

Entry
Database: EMDB / ID: EMD-1714
TitleAsymmetric structure of the empty Prochlorococcus Cyanophage P-SSP7
Map dataAsymmetric structure of the empty Prochlorococcus Cyanophage P-SSP7
Sample
  • Sample: Empty cyanophage P-SSP7
  • Virus: Prochlorococcus phage P-SSP7 (virus)
KeywordsMarine Podovirus / T7-like virus / Prochlorococcus MED4
Biological speciesProchlorococcus phage P-SSP7 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 24.0 Å
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
DepositionApr 28, 2010-
Header (metadata) releaseJun 11, 2010-
Map releaseJun 11, 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

pssp7-empty-...

Downloads & links

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Map

FileDownload / File: emd_1714.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric structure of the empty Prochlorococcus Cyanophage P-SSP7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.34 Å/pix.
x 480 pix.
= 1123.2 Å		2.34 Å/pix.
x 480 pix.
= 1123.2 Å		2.34 Å/pix.
x 480 pix.
= 1123.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.25109 - 3.12401
Average (Standard dev.)0.0285824 (±0.182937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 1123.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.342.342.34
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z1123.2001123.2001123.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-1.2513.1240.029

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Supplemental data

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Sample components

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Entire : Empty cyanophage P-SSP7

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

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Supramolecule #1000: Empty cyanophage P-SSP7

SupramoleculeName: Empty cyanophage P-SSP7 / 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: Cyanophage
Details: Viral particle containing portal (gp8), capsid (gp10), adaptor (gp11), nozzle (gp12), tail fibers (gp17) proteins.
NCBI-ID: 268748 / Sci species name: Prochlorococcus phage P-SSP7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Cyanophage
Host (natural)Organism: Prochlorococcus (bacteria) / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5 / Details: 100 mM Tris-HCl, 100 mM MgSO4, 30 mM NaCl
StainingType: NEGATIVE / Details: No stain
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 2 seconds 2 times before plunging.

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 4.5 K / Max: 102 K / Average: 101 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsMDS
DateAug 31, 2007
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: 1059 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA
Details: The map was directly reconstructed from raw particle images without imposing any symmetry.
Number images used: 1200
Final angle assignmentDetails: EMAN: Z axis along 5-fold and Y axis along 2-fold asymmetry axis.

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