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- EMDB-77283: Canine circovirus virus-like particle with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-77283
TitleCanine circovirus virus-like particle with DNA
Map dataRefinement map
Sample
  • Complex: An icosahedral virus-like particle composed of the canine circovirus Cap protein
    • Protein or peptide: Capsid protein
KeywordsCapsid / virus / jelly-roll / 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 / DNA binding
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein
Similarity search - Domain/homology
Biological speciesCanine circovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsHardy JM / Das S / Costin A / Raidal S / Forwood JK / Coulibaly FJ
Funding support Australia, 1 items
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 FJ / Forwood JK
History
DepositionMay 22, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77283.png

Downloads & links

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Map

FileDownload / File: emd_77283.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.09 Å/pix.
x 128 pix.
= 267.264 Å		2.09 Å/pix.
x 128 pix.
= 267.264 Å		2.09 Å/pix.
x 128 pix.
= 267.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-0.6221107 - 2.0671198
Average (Standard dev.)0.039434947 (±0.6130314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 267.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_77283_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_77283_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : An icosahedral virus-like particle composed of the canine circovi...

EntireName: An icosahedral virus-like particle composed of the canine circovirus Cap protein
Components
  • Complex: An icosahedral virus-like particle composed of the canine circovirus Cap protein
    • Protein or peptide: Capsid protein

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Supramolecule #1: An icosahedral virus-like particle composed of the canine circovi...

SupramoleculeName: An icosahedral virus-like particle composed of the canine circovirus Cap protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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.
Source (natural)Organism: Canine circovirus / Strain: Isolate 214
Molecular weightTheoretical: 1.87 MDa

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Canine circovirus / Strain: Isolate 214
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SRRHARASRR NYRTRPLNRY RRRRQNRFKL FHLRLRRTLT ADWPTAPVKP TNDPQTETPL LWNFDHLSFK LTDFLQASHG TGDFQHLPP FRFYKFKKVY IRARWINWPK TLMENVLGRT ALDLDGEDQG RGNATRSHLD PGTVPGRLEP PKDPNKAPFI Y DPLQDRSS ...String:
SRRHARASRR NYRTRPLNRY RRRRQNRFKL FHLRLRRTLT ADWPTAPVKP TNDPQTETPL LWNFDHLSFK LTDFLQASHG TGDFQHLPP FRFYKFKKVY IRARWINWPK TLMENVLGRT ALDLDGEDQG RGNATRSHLD PGTVPGRLEP PKDPNKAPFI Y DPLQDRSS SRSFNMATGF KRGLTPKPMF TQDITSPSAT APWLTRGTPW VSVIQGANMV WNGLSISLRQ MKDMRPTTPD TS TSQIPQV QYDISAYIAF KEFDYETGRQ L

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

Concentration9.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 1 s incubation time, blot time of 2 s, blot force of -2 and no drain time.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-18 / Number grids imaged: 1 / Number real images: 304 / Average exposure time: 7.2 sec. / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
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: 32271 / Details: Blob picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1)
Details: Defocus values were estimated using patch CTF estimation, and CTF correction was performed during 3D reconstruction
Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model / Details: Ab-initio model was generated in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1)
Details: Final reconstruction was generated using homogenous refinement in cryoSPARC.
Number images used: 1466
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: Homogenous refinement in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: Homogenous refinement in cryoSPARC
Final 3D classificationNumber classes: 4 / Avg.num./class: 7123 / Software - Name: cryoSPARC (ver. 4.3.1)
Details: The largest class contained 26,891 particles without DNA (deposited separately), and the second class contained 1,466 particles with DNA (this deposition). The other 2 classes contained 138 ...Details: The largest class contained 26,891 particles without DNA (deposited separately), and the second class contained 1,466 particles with DNA (this deposition). The other 2 classes contained 138 low-quality particles.
FSC plot (resolution estimation)

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