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- EMDB-35594: Cryo-EM reconstruction of PBCV-1 capsid block 8 -

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Basic information

Entry
Database: EMDB / ID: EMD-35594
TitleCryo-EM reconstruction of PBCV-1 capsid block 8
Map data
Sample
  • Virus: Paramecium bursaria Chlorella virus 1
Keywordsgiant virus / nucleocytoplasmic large DNA viruses (NCLDVs) / viral assembly / Paramecium bursaria chlorella virus 1 (PBCV-1) / chlorovirus / major capsid protein / minor capsid protein / VIRUS / VIRAL PROTEIN
Biological speciesParamecium bursaria Chlorella virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsShao Q / Agarkova IV / Noel EA / Dunigan DD / Liu Y / Wang A / Guo M / Xie L / Zhao X / Rossmann MG ...Shao Q / Agarkova IV / Noel EA / Dunigan DD / Liu Y / Wang A / Guo M / Xie L / Zhao X / Rossmann MG / Van Etten JL / Klose T / Fang Q
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1736030 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2022
Title: Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1.
Authors: Qianqian Shao / Irina V Agarkova / Eric A Noel / David D Dunigan / Yunshu Liu / Aohan Wang / Mingcheng Guo / Linlin Xie / Xinyue Zhao / Michael G Rossmann / James L Van Etten / Thomas Klose / Qianglin Fang /
Abstract: Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play ...Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.
History
DepositionMar 9, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35594.png

Downloads & links

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Map

FileDownload / File: emd_35594.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 448 pix.
= 725.76 Å		1.62 Å/pix.
x 448 pix.
= 725.76 Å		1.62 Å/pix.
x 448 pix.
= 725.76 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7
Minimum - Maximum-13.671996999999999 - 20.239439000000001
Average (Standard dev.)0.018998224 (±1.0236819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-660-122-79
Dimensions448448448
Spacing448448448
CellA=B=C: 725.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35594_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_35594_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35594_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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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 / Macromolecule list: #1-#26 / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 24.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5384

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56500
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
FSC plot (resolution estimation)

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