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- EMDB-4979: bat circovirus without DNA VLP -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-4979
Titlebat circovirus without DNA VLP
Map databat circovirus without DNA VLP
Sample
  • Virus: Bat circovirus
    • Protein or peptide: bat circovirus capsid protein
Keywordsbat circovirus without 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
Biological speciesBat circovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsForwood JK / Luque D
CitationJournal: To Be Published
Title: bat circovirus without 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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rpo
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rpo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4979.png

Downloads & links

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Map

FileDownload / File: emd_4979.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbat circovirus without DNA VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 260 pix.
= 275.6 Å		1.06 Å/pix.
x 260 pix.
= 275.6 Å		1.06 Å/pix.
x 260 pix.
= 275.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.04
Minimum - Maximum-0.16622324 - 0.27432784
Average (Standard dev.)0.0004025998 (±0.01885979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-130-130-130
Dimensions260260260
Spacing260260260
CellA=B=C: 275.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z275.600275.600275.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-130-130-130
NC/NR/NS260260260
D min/max/mean-0.1660.2740.000

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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: bat circovirus 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: Yes
Molecular weightTheoretical: 1.42 MDa
Virus shellShell ID: 1 / Diameter: 200.0 Å / T number (triangulation number): 1

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Macromolecule #1: bat circovirus capsid protein

MacromoleculeName: bat circovirus capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bat circovirus
Molecular weightTheoretical: 27.754744 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVYRRRRGRG RRARPMSSLG RLLYRKPWLM HPRFRARYRW RRKNGITNLR LTRQVELWVP KDAANASFYV NHYTFDLDDF IPAGTQLNS SPLPFKYYRI RKVKVEFQPR LPITSPFRGY GSTVPILDGA FVTPATGESD PIWDPYINFS GRHVIRTPAW Y HKRYFTPK ...String:
MVYRRRRGRG RRARPMSSLG RLLYRKPWLM HPRFRARYRW RRKNGITNLR LTRQVELWVP KDAANASFYV NHYTFDLDDF IPAGTQLNS SPLPFKYYRI RKVKVEFQPR LPITSPFRGY GSTVPILDGA FVTPATGESD PIWDPYINFS GRHVIRTPAW Y HKRYFTPK PLIDGNTGFF QPNNKQNALW FPNKQGQNIQ WSGLGFAMQK GNEAYNYQVR FTLYVQFREF DLFNN

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1474 / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 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: 0.75 µm / Nominal magnification: 47170
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

Particle selectionNumber selected: 124275
Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 58147
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: 83
Output model

PDB-6rpo:
bat circovirus without DNA VLP

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