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- EMDB-8606: Bacteriophage P22 mature virion capsid protein -

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Basic information

Database: EMDB / ID: 8606
TitleBacteriophage P22 mature virion capsid protein
SampleEnterobacteria phage P22
SourceEnterobacteria phage P22 / virus
Map dataBacteriophage P22 mature virion capsid protein, combined map
Methodsingle particle (icosahedral) reconstruction, at 3.3 Å resolution
AuthorsHryc CF / Chen D-H
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 3103-3108

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 3103-3108 Yorodumi Papers
Accurate model annotation of a near-atomic resolution cryo-EM map.
Corey F Hryc / Dong-Hua Chen / Pavel V Afonine / Joanita Jakana / Zhao Wang / Cameron Haase-Pettingell / Wen Jiang / Paul D Adams / Jonathan A King / Michael F Schmid / Wah Chiu

Validation ReportPDB-ID: 5uu5

SummaryFull reportAbout validation report
DateDeposition: Feb 16, 2017 / Header (metadata) release: Mar 15, 2017 / Map release: Mar 15, 2017 / Last update: Apr 5, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 9
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5uu5
  • Surface level: 9
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5uu5
  • Imaged by Jmol
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8606.map.gz (map file in CCP4 format, 2579891 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
864 pix
1.07 Å/pix.
= 924.48 Å
864 pix
1.07 Å/pix.
= 924.48 Å
864 pix
1.07 Å/pix.
= 924.48 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.07 Å
Contour Level:9 (by author), 9 (movie #1):
Minimum - Maximum-19.182793 - 38.868706
Average (Standard dev.)0.15328377 (1.9640912)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 924.48004 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z864864864
origin x/y/z0.0000.0000.000
length x/y/z924.480924.480924.480
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS-432-432-432
D min/max/mean-19.18338.8690.153

Supplemental data

Sample components

Entire Enterobacteria phage P22

EntireName: Enterobacteria phage P22 / Number of components: 2
MassTheoretical: 327.57294 MDa

Component #1: virus, Enterobacteria phage P22

VirusName: Enterobacteria phage P22 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 327.57294 MDa
SpeciesSpecies: Enterobacteria phage P22 / virus
Source (engineered)Expression System: Salmonella enterica subsp. enterica serovar typhimurium / bacteria
Shell #1Name of element: Capsid / Diameter: 735 Å / T number(triangulation number): 7

Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Recombinant expression: No
MassTheoretical: 46.795613 kDa
Source (engineered)Expression System: Salmonella phage P22 / virus

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 50 mM Tris, pH 7.6, 1 mM MgCl2, 25 mM NaCl / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 % / Details: single blot, one second duration

Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Details: normal alignment
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm / Energy filter: Omega energy filter / Energy window: 0-20 eV
Specimen HolderModel: JEOL 3200FSC CRYOHOLDER / Temperature: K ( 86 - 87 K)
CameraDetector: OTHER

Image acquisition

Image acquisitionNumber of digital images: 2927 / Sampling size: 6.4 microns
Raw dataEMPIAR-10083 (Title: Bacteriophage P22 mature virion capsid protein / Data size: 159.4
Data #1: Corrected images of P22 Mature Phage [picked particles - single frame - processed])

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 45150
Details: Movie-mode data was drift-corrected and damage-compensated using the program DE_process_frames.py.
3D reconstructionSoftware: JSPR
CTF correction: Per frame or incoherent sum of particle images, using CTFfind3
Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: All the selected 45,150 particle images were first shrunk by a factor of four to a box size of 216x216 in order to accelerate the data processing at low resolutions. About 2,100 shrunken particle images with largest defocuses were selected from each subset to build the initial template, again using the program JSPR. Five sets of 300 particle images were randomly selected from the highly-defocused 2,100 particle images of each subset, then the global orientation search was performed using JSPR for 20 iterations. The maps from each set were visually examined, and one of the converged maps was selected from the last iterations of each subset. This map was then used as the initial template for the global orientation search for all four-times-shrunken particle images. Several global orientation searches were carried out for the four-times-shrunken data until the resolution converged, as judged by the Fourier Shell Correlation (FSC) curve of two independent data sets (the best 11,000 particles of each). The subsequent local orientation determination was performed using data up to a resolution slightly lower than the resolution assessed by the Gold Standard FSC = 0.143 criterion from the previous iteration, until resolution experienced no further improvement. The orientations and centers for the four-times-shrunken data were then migrated to the full-size (864x864) particle images for additional orientation determination. It should be noted the first frame was removed from all images and that orientation determination was done with all 23 remaining frames. We then experimented with different sets of subframes of the same particle data set and assessed the density connectivity and resolvability within these different maps. Once this was complete, we found empirically that using frames 1 through 6 (dose of ~10 e/A2), with both motion and damage corrections, yielded the best resolved density map, with a resolution of 3.3 Angstrom based on the Gold Standard estimate. The final reconstruction was produced from the best ~50% of the total particle images. The amplitude of all cryoEM density maps for visualization was scaled to the X-ray structure of bacteriophage HK97 mature capsid (PDB ID: 1OHG) and low-pass filtered to ~3.0 Angstrom resolution.
Euler angles: Jiang labs Single Particle Reconstruction (JSPR): 45,150 particle images were used towards 3 Angstrom resolution. During the last several iterations, defocus, astigmatism, and magnification parameters were refined together with the orientation and center position for each particle image.
FSC plot (resolution assessment)

Atomic model buiding

Output model

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