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- EMDB-1339: Genome sequence, structural proteins, and capsid organization of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1339
TitleGenome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus.
Map dataBacteriophage Syn5
Sample
  • Sample: Syn5
  • Virus: Synechococcus phage Syn5 (virus)
Biological speciesSynechococcus phage Syn5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsPope WH / Weigele PR / Chang J / Pedulla ML / Ford ME / Houtz JM / Jiang W / Chiu W / Hatfull GF / Hendrix RW / King J
CitationJournal: J Mol Biol / Year: 2007
Title: Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus.
Authors: Welkin H Pope / Peter R Weigele / Juan Chang / Marisa L Pedulla / Michael E Ford / Jennifer M Houtz / Wen Jiang / Wah Chiu / Graham F Hatfull / Roger W Hendrix / Jonathan King /
Abstract: Marine Synechococcus spp and marine Prochlorococcus spp are numerically dominant photoautotrophs in the open oceans and contributors to the global carbon cycle. Syn5 is a short-tailed cyanophage ...Marine Synechococcus spp and marine Prochlorococcus spp are numerically dominant photoautotrophs in the open oceans and contributors to the global carbon cycle. Syn5 is a short-tailed cyanophage isolated from the Sargasso Sea on Synechococcus strain WH8109. Syn5 has been grown in WH8109 to high titer in the laboratory and purified and concentrated retaining infectivity. Genome sequencing and annotation of Syn5 revealed that the linear genome is 46,214 bp with a 237 bp terminal direct repeat. Sixty-one open reading frames (ORFs) were identified. Based on genomic organization and sequence similarity to known protein sequences within GenBank, Syn5 shares features with T7-like phages. The presence of a putative integrase suggests access to a temperate life cycle. Assignment of 11 ORFs to structural proteins found within the phage virion was confirmed by mass-spectrometry and N-terminal sequencing. Eight of these identified structural proteins exhibited amino acid sequence similarity to enteric phage proteins. The remaining three virion proteins did not resemble any known phage sequences in GenBank as of August 2006. Cryo-electron micrographs of purified Syn5 virions revealed that the capsid has a single "horn", a novel fibrous structure protruding from the opposing end of the capsid from the tail of the virion. The tail appendage displayed an apparent 3-fold rather than 6-fold symmetry. An 18 A resolution icosahedral reconstruction of the capsid revealed a T=7 lattice, but with an unusual pattern of surface knobs. This phage/host system should allow detailed investigation of the physiology and biochemistry of phage propagation in marine photosynthetic bacteria.
History
DepositionMar 9, 2007-
Header (metadata) releaseMar 9, 2007-
Map releaseMar 9, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.746914829
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.746914829
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1339.gif

Downloads & links

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Map

FileDownload / File: emd_1339.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage Syn5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.43 Å/pix.
x 144 pix.
= 781.92 Å		5.43 Å/pix.
x 144 pix.
= 781.92 Å		5.43 Å/pix.
x 144 pix.
= 781.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.43 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 3.57 / Movie #1: 1.7469148
Minimum - Maximum-10.248900000000001 - 23.807700000000001
Average (Standard dev.)0.13807 (±2.3099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 781.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.435.435.43
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z781.920781.920781.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-10.24923.8080.138

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Supplemental data

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Sample components

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Entire : Syn5

EntireName: Syn5
Components
  • Sample: Syn5
  • Virus: Synechococcus phage Syn5 (virus)

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Supramolecule #1000: Syn5

SupramoleculeName: Syn5 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Synechococcus phage Syn5

SupramoleculeName: Synechococcus phage Syn5 / type: virus / ID: 1 / Name.synonym: Cyanophage Syn5 / NCBI-ID: 438482 / Sci species name: Synechococcus phage Syn5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Cyanophage Syn5
Host (natural)Organism: Synechococcus (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid / Diameter: 600 Å / T number (triangulation number): 7

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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: 8 / Details: 100mM NaCl, 100mM MgCl2, 50mM Tris
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Details55360 magnification on CCD
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SAVR / Number images used: 2616

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