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- EMDB-1693: Cryo-EM reconstruction of Phage Gifsy-2 expanded procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-1693
TitleCryo-EM reconstruction of Phage Gifsy-2 expanded procapsid
Map dataGifsy-2 expanded procapsid
Sample
  • Sample: Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium
  • Virus: Phage Gifsy-2 (virus)
KeywordsBacteriophage / Gifsy-2 / capsid
Biological speciesPhage Gifsy-2 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.3 Å
AuthorsEffantin G / Figueroa-Bossi N / Schoehn G / Bossi L / Conway JF
CitationJournal: Virology / Year: 2010
Title: The tripartite capsid gene of Salmonella phage Gifsy-2 yields a capsid assembly pathway engaging features from HK97 and lambda.
Authors: Grégory Effantin / Nara Figueroa-Bossi / Guy Schoehn / Lionello Bossi / James F Conway /
Abstract: Phage Gifsy-2, a lambdoid phage infecting Salmonella, has an unusually large composite gene coding for its major capsid protein (mcp) at the C-terminal end, a ClpP-like protease at the N-terminus, ...Phage Gifsy-2, a lambdoid phage infecting Salmonella, has an unusually large composite gene coding for its major capsid protein (mcp) at the C-terminal end, a ClpP-like protease at the N-terminus, and a approximately 200 residue central domain of unknown function but which may have a scaffolding role. This combination of functions on a single coding region is more extensive than those observed in other phages such as HK97 (scaffold-capsid fusion) and lambda (protease-scaffold fusion). To study the structural phenotype of the unique Gifsy-2 capsid gene, we have purified Gifsy-2 particles and visualized capsids and procapsids by cryoelectron microscopy, determining structures to resolutions up to 12A. The capsids have lambdoid T=7 geometry and are well modeled with the atomic structures of HK97 mcp and phage lambda gpD decoration protein. Thus, the unique Gifsy-2 capsid protein gene yields a capsid maturation pathway engaging features from both phages HK97 and lambda.
History
DepositionJan 25, 2010-
Header (metadata) releaseApr 9, 2010-
Map releaseJan 28, 2011-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 110
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 110
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1693.png

Downloads & links

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Map

FileDownload / File: emd_1693.map.gz / Format: CCP4 / Size: 129.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationGifsy-2 expanded procapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.84 Å/pix.
x 411 pix.
= 410.766 Å		1.84 Å/pix.
x 411 pix.
= 410.766 Å		1.84 Å/pix.
x 411 pix.
= 410.766 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 110.0 / Movie #1: 110
Minimum - Maximum-231.0 - 447.0
Average (Standard dev.)2.25031 (±62.774500000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions411411411
Spacing411411411
CellA=B=C: 410.766 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.8421.8421.842
M x/y/z223223223
origin x/y/z0.0000.0000.000
length x/y/z410.766410.766410.766
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS411411411
D min/max/mean-231.000447.0002.250

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Supplemental data

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Sample components

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Entire : Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium

EntireName: Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium
Components
  • Sample: Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium
  • Virus: Phage Gifsy-2 (virus)

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Supramolecule #1000: Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium

SupramoleculeName: Bacteriophage Gifsy-2 capsid purified from Salmonella Typhimurium
type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1

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Supramolecule #1: Phage Gifsy-2

SupramoleculeName: Phage Gifsy-2 / type: virus / ID: 1 / Name.synonym: Gifsy-2 / NCBI-ID: 129862 / Sci species name: Phage Gifsy-2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Gifsy-2
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 630 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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 10 mM Tris-HCl.pH7.5, 10 mM MgSO4
StainingType: NEGATIVE / Details: Ammo
GridDetails: 300 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made manual plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.84 µm / Number real images: 51
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.3 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: pft - em3dr / Number images used: 3281

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