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- EMDB-8144: Faustovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-8144
TitleFaustovirus
Map dataNone
Sample
  • Virus: Faustovirus
    • Protein or peptide: major capsid protein
Function / homologyGroup II dsDNA virus coat/capsid protein / Putative major capsid protein p72
Function and homology information
Biological speciesFaustovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 15.5 Å
AuthorsKlose T / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 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 11, 2016-
Header (metadata) releaseApr 20, 2016-
Map releaseMay 18, 2016-
UpdateApr 13, 2022-
Current statusApr 13, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5j7v
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5j7v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8144.png

Downloads & links

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Map

FileDownload / File: emd_8144.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 3032. Å		7.58 Å/pix.
x 400 pix.
= 3032. Å		7.58 Å/pix.
x 400 pix.
= 3032. 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: 10.0 / Movie #1: 10
Minimum - Maximum-42.700462 - 49.291286
Average (Standard dev.)0.53756297 (±4.6943564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 3032.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.587.587.58
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z3032.0003032.0003032.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-42.70049.2910.538

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Supplemental data

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Sample components

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Entire : Faustovirus

EntireName: Faustovirus
Components
  • Virus: Faustovirus
    • Protein or peptide: major capsid protein

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Supramolecule #1: Faustovirus

SupramoleculeName: Faustovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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: outer capsid shell / Diameter: 2600.0 Å / T number (triangulation number): 277
Virus shellShell ID: 2 / Name: inner capsid shell / Diameter: 1900.0 Å / T number (triangulation number): 16

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Macromolecule #1: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Faustovirus
Molecular weightTheoretical: 71.781891 KDa
SequenceString: EAGGVFKLIA NDGKADRMIM ANDLLNDRIK SIMCLRAKQG FSDPTPTLVD IERTHILLIN SHYKPFAAMG YEYQKTRPNT GNPTYNSTI QFSIPQFGDF FSDMVVHVQL AATSASAGTV PALPAFIGAD DQVLTSTSVV SATENTTSGV YTLYTQSYVN Q QGTTQTVA ...String:
EAGGVFKLIA NDGKADRMIM ANDLLNDRIK SIMCLRAKQG FSDPTPTLVD IERTHILLIN SHYKPFAAMG YEYQKTRPNT GNPTYNSTI QFSIPQFGDF FSDMVVHVQL AATSASAGTV PALPAFIGAD DQVLTSTSVV SATENTTSGV YTLYTQSYVN Q QGTTQTVA AAATNFVRYC EYPGLRLFKR VKFEVNGNPL DEYTALAAIM YNKFHVPDFK LTGWKRLIGQ EVPVEAASNL VN IASTTPW GSPIVALSDV NGTAVTGSPV NAAITARKLT QVVFGAQTPK ATQEQLNMFV PLLFWFRDPR LAIASVSIPY GQR FITVDI EQQSNILFTA PGNLFLQTTV ETLLTTGAGK GTATGVLLTQ YNRYTTYTPT LASGSSIDGT QAVQNIELYI NNIF VTPEI HDIYIKRIGF TLIRVYREQV QREVNAADQV LQSQLKWPVE FIYLGLRPAN NIAAGNTYQW RDWHHLTSVT NEPVY DVSQ SYARVSIDDT VAPVGSTTFK QSASQVMQNQ YIVPVETETL DTVRVKAHGI ELYAQYRAQF YRDYIPWNYG SFNLVT PQD KGALFLNFCL YPGTYQPSGH VNISRAREFY IEYTSSFCDS SNPCDLISIA KCINFLLISD GSAVLRYSTK EFYLQCL IL RCI

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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 / Instrument: GATAN CRYOPLUNGE 3 / Details: Plunged into liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER / Details: Random angle assignment
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 9640
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5j7o

chain_id: A

5j7o

chain_id: B

5j7o

chain_id: C
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-5j7v:
Faustovirus major capsid protein

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