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- EMDB-8488: Bacteriophage PAU -

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Basic information

Database: EMDB / ID: 8488
TitleBacteriophage PAU
Samplebacteriophage PAU
Sourcebacteriophage PAU / virus
Map dataBacteriophage PAU
Methodsingle particle reconstruction, at 9 Å resolution
AuthorsHua J / Huet A / Lopez CA / Toropova K / Pope WH / Duda RL / Hendrix RW / Conway JF
CitationMBio, 2017, 8

MBio, 2017, 8 Yorodumi Papers
Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold.
Jianfei Hua / Alexis Huet / Carlos A Lopez / Katerina Toropova / Welkin H Pope / Robert L Duda / Roger W Hendrix / James F Conway

DateDeposition: Nov 29, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Nov 1, 2017 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_8488.map.gz (map file in CCP4 format, 357259 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
447 pix
3.26 Å/pix.
= 1457.22 Å
447 pix
3.26 Å/pix.
= 1457.22 Å
447 pix
3.26 Å/pix.
= 1457.22 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.26 Å
Contour Level:6 (by author), 6 (movie #1):
Minimum - Maximum-11.3698 - 25.197752
Average (Standard dev.)0.21042891 (2.2242575)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1457.22 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z447447447
origin x/y/z0.0000.0000.000
length x/y/z1457.2201457.2201457.220
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-11.37025.1980.210

Supplemental data

Sample components

Entire bacteriophage PAU

EntireName: bacteriophage PAU / Number of components: 1

Component #1: virus, bacteriophage PAU

VirusName: bacteriophage PAU / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: bacteriophage PAU / virus
Source (natural)Host Species: Sphingomonas paucimobilis / bacteria /
Shell #1Name of element: capsid / Diameter: 1120 Å / T number(triangulation number): 25

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.9
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 5000 nm
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 177 / Sampling size: 6.35 microns

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 9260
3D reconstructionSoftware: Auto3DEM / Resolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

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