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- PDB-9yz1: Structure of a canine circovirus virus-like particle -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9yz1
TitleStructure of a canine circovirus virus-like particle
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / Capsid / virus / jelly-roll
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 / DNA binding
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein
Similarity search - Domain/homology
Biological speciesCanine circovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsHardy, J.M. / Das, S. / Costin, A. / Raidal, S. / Forwood, J.K. / Coulibaly, F.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: To Be Published
Title: Structural characterization of bat and canine circoviruses reveal unique motifs and minimal region required for assembly
Authors: Coulibaly, F.J. / Forwood, J.K.
History
DepositionOct 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)31,2291
Polymers31,2291
Non-polymers00
Water00
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,873,76860
Polymers1,873,76860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein


Mass: 31229.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine circovirus / Strain: Isolate 214 / Production host: Escherichia coli (E. coli) / References: UniProt: I3VPR5
Has protein modificationN

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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: An icosahedral virus-like particle composed of the canine circovirus Cap protein
Type: COMPLEX
Details: Cap protein was recombinantly expressed and purified from E. coli in a pMSCG21 vector with an N-terminal His-tag followed by a linker and a TEV cleavage site. The His-tag was cleaved off ...Details: Cap protein was recombinantly expressed and purified from E. coli in a pMSCG21 vector with an N-terminal His-tag followed by a linker and a TEV cleavage site. The His-tag was cleaved off before cryo-EM experiments.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.87 MDa / Experimental value: NO
Source (natural)Organism: Canine circovirus / Strain: Isolate 214
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 9.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: 1 s incubation time, blot time of 2 s, blot force of -2 and no drain time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.2 sec. / Electron dose: 57 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 304
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansMovie frames/image: 18 / Used frames/image: 1-18

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2EPU1image acquisition
4cryoSPARC4.3.1CTF correction
7ISOLDE1.6.0model fitting
8Coot0.9.8.3model fitting
9UCSF ChimeraX1.6.1model fitting
11cryoSPARC4.3.1initial Euler assignment
12cryoSPARC4.3.1final Euler assignment
13cryoSPARC4.3.1classification
14cryoSPARC4.3.13D reconstruction
15PHENIX1.20.1_4887model refinement
CTF correctionDetails: Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction
Type: NONE
Particle selectionNum. of particles selected: 32271 / Details: Blob picking
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26891 / Algorithm: BACK PROJECTION
Details: Final reconstruction was generated using homogenous refinement in cryoSPARC, and sharpened locally using DeepEMhancer
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in Phenix.
Atomic model buildingPDB-ID: 5J36

5j36


Pdb chain-ID: A / Accession code: 5J36 / Chain residue range: 25-257 / Pdb chain residue range: 25-257 / Source name: PDB / Type: experimental model

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