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- EMDB-4977: non-expanded bat circovirus with DNA VLP -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-4977
Titlenon-expanded bat circovirus with DNA VLP
Map dataBat circovirus DNA non-expanded class (class01)
Sample
  • Virus: Bat circovirus
    • Protein or peptide: Capsid protein
Keywordsnon-expanded bat circovirus with DNA VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


viral capsid assembly / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein
Similarity search - Domain/homology
Capsid protein / Capsid protein
Similarity search - Component
Biological speciesBat circovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsForwood JK / Luque D
CitationJournal: To Be Published
Title: non-expanded bat circovirus with DNA VLP
Authors: Forwood JK / Luque D / Mata CP / Das S / Raidal S
History
DepositionMay 14, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseNov 25, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rpk
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rpk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4977.png

Downloads & links

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Map

FileDownload / File: emd_4977.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBat circovirus DNA non-expanded class (class01)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 200 pix.
= 274. Å		1.37 Å/pix.
x 200 pix.
= 274. Å		1.37 Å/pix.
x 200 pix.
= 274. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.6383743 - 0.97930515
Average (Standard dev.)0.0014359879 (±0.07130003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 274.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z274.000274.000274.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.6380.9790.001

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Supplemental data

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Sample components

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Entire : Bat circovirus

EntireName: Bat circovirus
Components
  • Virus: Bat circovirus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Bat circovirus

SupramoleculeName: Bat circovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1329650 / Sci species name: Bat circovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 1.42 MDa
Virus shellShell ID: 1 / Diameter: 200.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bat circovirus
Molecular weightTheoretical: 23.749828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RFRARYRWRR KNGITNLRLT RQVELWVPKD AANASFYVNH YTFDLDDFIP AGTQLNSSPL PFKYYRIRKV KVEFQPRLPI TSPFRGYGS TVPILDGAFV TPATGESDPI WDPYINFSGR HVIRTPAWYH KRYFTPKPLI DGNTGFFQPN NKQNALWFPN K QGQNIQWS ...String:
RFRARYRWRR KNGITNLRLT RQVELWVPKD AANASFYVNH YTFDLDDFIP AGTQLNSSPL PFKYYRIRKV KVEFQPRLPI TSPFRGYGS TVPILDGAFV TPATGESDPI WDPYINFSGR HVIRTPAWYH KRYFTPKPLI DGNTGFFQPN NKQNALWFPN K QGQNIQWS GLGFAMQKGN EAYNYQVRFT LYVQFREFDL FNN

UniProtKB: Capsid protein

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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: 8
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 524 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 195079
Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 56911
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 97
Output model

PDB-6rpk:
non-expanded bat circovirus with DNA VLP

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