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- EMDB-7626: An asymmetric unit of the icosahedrally averaged outer capsid she... -

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Basic information

Entry
Database: EMDB / ID: EMD-7626
TitleAn asymmetric unit of the icosahedrally averaged outer capsid shell of PBCV-1
Map dataThe outer capsid shell of PBCV-1
Sample
  • Virus: Paramecium bursaria Chlorella virus 1
Biological speciesParamecium bursaria Chlorella virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFang Q / Rossmann MG
CitationJournal: Nat Commun / Year: 2018
Title: Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions.
Authors: Dongjie Zhu / Xiangxi Wang / Qianglin Fang / James L Van Etten / Michael G Rossmann / Zihe Rao / Xinzheng Zhang /
Abstract: The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a ...The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a "block-based" reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.
History
DepositionMar 26, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 2, 2018-
UpdateMay 2, 2018-
Current statusMay 2, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.163
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.163
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7626.png

Downloads & links

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Map

FileDownload / File: emd_7626.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe outer capsid shell of PBCV-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 420 pix.
= 680.4 Å		1.62 Å/pix.
x 420 pix.
= 680.4 Å		1.62 Å/pix.
x 420 pix.
= 680.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.163 / Movie #1: 0.163
Minimum - Maximum-0.7860655 - 1.0247275
Average (Standard dev.)0.00010024339 (±0.038591363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 680.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z680.400680.400680.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.7861.0250.000

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Supplemental data

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Sample components

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Entire : Paramecium bursaria Chlorella virus 1

EntireName: Paramecium bursaria Chlorella virus 1
Components
  • Virus: Paramecium bursaria Chlorella virus 1

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Supramolecule #1: Paramecium bursaria Chlorella virus 1

SupramoleculeName: Paramecium bursaria Chlorella virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chlorella variabilis (plant)
Virus shellShell ID: 1 / Name: outer capsid shell / Diameter: 1850.0 Å / T number (triangulation number): 169

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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

Concentration20 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 85.0 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 24.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5378

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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