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- EMDB-5332: The cryoEM structure of the bacteriophage phiKZ polysheath -

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Basic information

Entry
Database: EMDB / ID: EMD-5332
TitleThe cryoEM structure of the bacteriophage phiKZ polysheath
Map dataThis is a map of phiKZ extended tail sheath
Sample
  • Sample: Bacteriophage phiKZ polysheath
  • Virus: Pseudomonas phage phiKZ (virus)
Keywordshomopolymer of the bacteriophage tail sheath protein
Function / homology: / Bacteriophage phiKZ, gp29PR / PHIKZ029
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsAksyuk AA / Kurochkina LP / Fokine A / Mesyanzhinov VV / Rossmann MG
CitationJournal: Structure / Year: 2011
Title: Structural conservation of the myoviridae phage tail sheath protein fold.
Authors: Anastasia A Aksyuk / Lidia P Kurochkina / Andrei Fokine / Farhad Forouhar / Vadim V Mesyanzhinov / Liang Tong / Michael G Rossmann /
Abstract: Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The ...Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.
History
DepositionAug 15, 2011-
Header (metadata) releaseAug 29, 2011-
Map releaseDec 6, 2011-
UpdateMar 19, 2012-
Current statusMar 19, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j0h
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5332.jpg

Downloads & links

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Map

FileDownload / File: emd_5332.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of phiKZ extended tail sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 140 pix.
= 593.6 Å		4.24 Å/pix.
x 140 pix.
= 593.6 Å		4.24 Å/pix.
x 140 pix.
= 593.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.36418533 - 8.04589081
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 593.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z593.600593.600593.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-5.3648.046-0.000

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Supplemental data

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Sample components

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Entire : Bacteriophage phiKZ polysheath

EntireName: Bacteriophage phiKZ polysheath
Components
  • Sample: Bacteriophage phiKZ polysheath
  • Virus: Pseudomonas phage phiKZ (virus)

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Supramolecule #1000: Bacteriophage phiKZ polysheath

SupramoleculeName: Bacteriophage phiKZ polysheath / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Name.synonym: tail sheath / Details: tail portion of the virion was selected / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: tail sheath
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / synonym: BACTERIA(EUBACTERIA)

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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 CM300FEG/HE
DateAug 16, 2004
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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