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- EMDB-6398: Electron cryo-microscopy of a Propionibacterium acnes phage -

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Basic information

Entry
Database: EMDB / ID: EMD-6398
TitleElectron cryo-microscopy of a Propionibacterium acnes phage
Map dataReconstruction of Propionibacterium acnes phage
Sample
  • Sample: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
  • Virus: Propionibacterium phage PA6 (virus)
Keywordsacne / bacteriophage / cryoEM / HK97-like
Function / homologyGp6
Function and homology information
Biological speciesPropionibacterium phage PA6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChiou J / Zhang X / Marinelli LJ / Modlin RL / Zhou ZH
CitationJournal: To Be Published
Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear
Authors: Chiou J / Zhang X / Marinelli LJ / Modlin RL / Zhou ZH
History
DepositionJul 23, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseJul 27, 2016-
UpdateJul 27, 2016-
Current statusJul 27, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0625
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0625
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jb5
  • Surface level: 0.0625
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jb5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6398.jpg

Downloads & links

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Map

FileDownload / File: emd_6398.map.gz / Format: CCP4 / Size: 523.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Propionibacterium acnes phage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 520 pix.
= 676. Å		1.3 Å/pix.
x 520 pix.
= 676. Å		1.3 Å/pix.
x 520 pix.
= 676. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0625 / Movie #1: 0.0625
Minimum - Maximum-0.18350838 - 0.23970643
Average (Standard dev.)-0.00263189 (±0.01325464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-260-260-260
Dimensions520520520
Spacing520520520
CellA=B=C: 676.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z520520520
origin x/y/z0.0000.0000.000
length x/y/z676.000676.000676.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-260-260-260
NC/NR/NS520520520
D min/max/mean-0.1840.240-0.003

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Supplemental data

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Sample components

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Entire : Propionibacterium acnes bacteriophage ATCC_Clear capsid structure

EntireName: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
Components
  • Sample: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
  • Virus: Propionibacterium phage PA6 (virus)

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Supramolecule #1000: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure

SupramoleculeName: Propionibacterium acnes bacteriophage ATCC_Clear capsid structure
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 33 MDa / Method: SDS-PAGE/MS

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Supramolecule #1: Propionibacterium phage PA6

SupramoleculeName: Propionibacterium phage PA6 / type: virus / ID: 1 / Name.synonym: Propionibacterium acnes bacteriophage / Details: Mature virions, DNA inside masked / NCBI-ID: 376758 / Sci species name: Propionibacterium phage PA6 / Sci species strain: ATCC 29399B_C / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Propionibacterium acnes bacteriophage
Host (natural)Organism: Propionibacterium acnes (bacteria) / Strain: 6919 / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 660 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

GridDetails: Purified sample was applied to a Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 15 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateMay 16, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 3168 / Average electron dose: 25 e/Å2
Details: Every image is the average of twelve frames recorded by the direct electron detector.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38462 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.27 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 38462
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using an in-house selection procedure.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 27504

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