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- EMDB-1476: Structure of a bacteriophage N4 mutant lacking gp65 -

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Basic information

Entry
Database: EMDB / ID: EMD-1476
TitleStructure of a bacteriophage N4 mutant lacking gp65
Map dataThis is an asymmetric reconstruction of a bacteriophage N4 mutant virus lacking gp65.
Sample
  • Sample: Bacteriophage N4 mutant lacking gp65
  • Virus: Enterobacteria phage N4 (virus)
KeywordsBacteriophage N4 / Podoviridae / non-contractile tail sheath / tail tube / appendages
Biological speciesEnterobacteria phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsChoi KH / McPartland J / Kaganman I / Bowman VD / Rothman-Denes LB / Rossmann MG
CitationJournal: J Mol Biol / Year: 2008
Title: Insight into DNA and protein transport in double-stranded DNA viruses: the structure of bacteriophage N4.
Authors: Kyung H Choi / Jennifer McPartland / Irene Kaganman / Valorie D Bowman / Lucia B Rothman-Denes / Michael G Rossmann /
Abstract: Bacteriophage N4 encapsidates a 3500-aa-long DNA-dependent RNA polymerase (vRNAP), which is injected into the host along with the N4 genome upon infection. The three-dimensional structures of wild- ...Bacteriophage N4 encapsidates a 3500-aa-long DNA-dependent RNA polymerase (vRNAP), which is injected into the host along with the N4 genome upon infection. The three-dimensional structures of wild-type and mutant N4 viruses lacking gp17, gp50, or gp65 were determined by cryoelectron microscopy. The virion has an icosahedral capsid with T=9 quasi-symmetry that encapsidates well-organized double-stranded DNA and vRNAP. The tail, attached at a unique pentameric vertex of the head, consists of a neck, 12 appendages, and six ribbons that constitute a non-contractile sheath around a central tail tube. Comparison of wild-type and mutant virus structures in conjunction with bioinformatics established the identity and virion locations of the major capsid protein (gp56), a decorating protein (gp17), the vRNAP (gp50), the tail sheath (gp65), the appendages (gp66), and the portal protein (gp59). The N4 virion organization provides insight into its assembly and suggests a mechanism for genome and vRNAP transport strategies utilized by this unique system.
History
DepositionFeb 22, 2008-
Header (metadata) releaseFeb 25, 2008-
Map releaseMar 31, 2009-
UpdateMar 31, 2009-
Current statusMar 31, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1476.gif

Downloads & links

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Map

FileDownload / File: emd_1476.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an asymmetric reconstruction of a bacteriophage N4 mutant virus lacking gp65.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.54 Å/pix.
x 420 pix.
= 1486.8 Å		3.54 Å/pix.
x 420 pix.
= 1486.8 Å		3.54 Å/pix.
x 420 pix.
= 1486.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.54 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.62 / Movie #1: 1.5
Minimum - Maximum-10.400600000000001 - 14.059699999999999
Average (Standard dev.)-0.000000000370159 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 1486.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.543.543.54
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z1486.8001486.8001486.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-10.40114.060-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage N4 mutant lacking gp65

EntireName: Bacteriophage N4 mutant lacking gp65
Components
  • Sample: Bacteriophage N4 mutant lacking gp65
  • Virus: Enterobacteria phage N4 (virus)

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Supramolecule #1000: Bacteriophage N4 mutant lacking gp65

SupramoleculeName: Bacteriophage N4 mutant lacking gp65 / type: sample / ID: 1000 / Number unique components: 9

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Supramolecule #1: Enterobacteria phage N4

SupramoleculeName: Enterobacteria phage N4 / type: virus / ID: 1 / Name.synonym: bacteriophage N4 / NCBI-ID: 10752 / Sci species name: Enterobacteria phage N4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage N4
Host (natural)synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 740 Å / T number (triangulation number): 9

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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

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.13 µm / Nominal magnification: 39500
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2096

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