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- EMDB-8145: Faustovirus inner capsid shell -

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Basic information

Entry
Database: EMDB / ID: EMD-8145
TitleFaustovirus inner capsid shell
Map dataNone
Sample
  • Virus: Faustovirus
Keywordsvirus / inner shell / VIRUS LIKE PARTICLE
Biological speciesFaustovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 26.4 Å
AuthorsKlose T / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI011219 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of faustovirus, a large dsDNA virus.
Authors: Thomas Klose / Dorine G Reteno / Samia Benamar / Adam Hollerbach / Philippe Colson / Bernard La Scola / Michael G Rossmann /
Abstract: Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that ...Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that has been found to use two protein shells to encapsidate and protect its genome. The crystal structure of the major capsid protein, in combination with cryo-electron microscopy structures of two different maturation stages of the virus, shows that the outer virus shell is composed of a double jelly-roll protein that can be found in many double-stranded DNA viruses. The structure of the repeating hexameric unit of the inner shell is different from all other known capsid proteins. In addition to the unique architecture, the region of the genome that encodes the major capsid protein stretches over 17,000 bp and contains a large number of introns and exons. This complexity might help the virus to rapidly adapt to new environments or hosts.
History
DepositionApr 6, 2016-
Header (metadata) releaseApr 20, 2016-
Map releaseMay 18, 2016-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8145.png

Downloads & links

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Map

FileDownload / File: emd_8145.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.58 Å/pix.
x 350 pix.
= 2653. Å		7.58 Å/pix.
x 350 pix.
= 2653. Å		7.58 Å/pix.
x 350 pix.
= 2653. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-11.933381000000001 - 18.716495999999999
Average (Standard dev.)0.20195952 (±1.5350035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-175-175-175
Dimensions350350350
Spacing350350350
CellA=B=C: 2653.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.587.587.58
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z2653.0002653.0002653.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS350350350
D min/max/mean-11.93318.7160.202

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Supplemental data

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Sample components

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Entire : Faustovirus

EntireName: Faustovirus
Components
  • Virus: Faustovirus

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Supramolecule #1: Faustovirus

SupramoleculeName: Faustovirus / type: virus / ID: 1 / Parent: 0
Details: Virus was isolated from Vermamoeba vermiformis and the inner shell was purified using density centrifugation.
NCBI-ID: 1477405 / Sci species name: Faustovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vermamoeba vermiformis (eukaryote) / Strain: CDC 19
Virus shellShell ID: 1 / Name: inner capsid shell / Diameter: 1900.0 Å / T number (triangulation number): 16

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
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: OTHER / Details: random angle assignment
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 26.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 1190
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
FSC plot (resolution estimation)

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