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

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Basic information

Entry
Database: PDB / ID: 6rpk
Titlenon-expanded bat circovirus with DNA VLP
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / non-expanded bat circovirus with DNA VLP
Function / homologyCircovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Capsid protein / Capsid protein
Function and homology information
Biological speciesBat circovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsForwood, J.K. / Luque, D. / Mata, C.P. / Das, S. / Raidal, S.
CitationJournal: To Be Published
Title: non-expanded bat circovirus with DNA VLP
Authors: Forwood, J.K. / Luque, D. / Mata, C.P. / Das, S. / Raidal, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4977
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
u: Capsid protein


Theoretical massNumber of molelcules
Total (without water)23,7501
Polymers23,7501
Non-polymers00
Water00
1
u: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,424,99060
Polymers1,424,99060
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
u: Capsid protein
x 5


  • icosahedral pentamer
  • 119 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)118,7495
Polymers118,7495
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
u: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 142 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)142,4996
Polymers142,4996
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein


Mass: 23749.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat circovirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G6IPQ0, UniProt: R4L4W6*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bat circovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.42 MDa / Experimental value: NO
Source (natural)Organism: Bat circovirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Virus shellDiameter: 200 nm / Triangulation number (T number): 1
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 73000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 524
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
1Gautomatchparticle selection
2EPUimage acquisition
4RELIONCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14Cootmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 195079
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56911 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 97 / Protocol: OTHER / Space: REAL

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