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- PDB-9s3s: Capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV),... -

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Basic information

Entry
Database: PDB / ID: 9s3s
TitleCapsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV), a CRESS-DNA bacilladnavirus
ComponentsHypothetical protein protein
KeywordsVIRUS / CRESS-DNA virus / Cressdnaviricota / Bacilladnaviridae / ClorDNAV / capsid structure / single-stranded DNA virus / jelly-roll / structural virology / virus evolution
Function / homologyShotokuvirus capsid protein / Hypothetical protein protein
Function and homology information
Biological speciesChaetoceros lorenzianus DNA virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsMunke, A. / Gebhard, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Carl Trygger Foundation23:2665 Sweden
CitationJournal: Virol J / Year: 2025
Title: Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling.
Authors: L Johanna Gebhard / Yuji Tomaru / Kenta Okamoto / Anna Munke /
Abstract: Viruses that infect single-celled algae strongly regulate microalgae growth and community composition through cell lysis, enable nutrient recycling in marine ecosystems, and offer valuable insights ...Viruses that infect single-celled algae strongly regulate microalgae growth and community composition through cell lysis, enable nutrient recycling in marine ecosystems, and offer valuable insights into early stages of viral evolution. One major group, the Bacilladnaviridae family of single-stranded DNA viruses, infects diatoms in marine environments. Here, we present the capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV, Protobacilladnavirus chaelor) determined at 2.2 Å resolution, thereby expanding the known structural diversity within the Cressdnaviricota phylum. The ClorDNAV capsid protein (CP) contains a conserved jelly-roll fold and a surface-exposed projection domain, with both N- and C-termini oriented toward the capsid interior. A low-resolution reconstruction of the genome revealed a spooled arrangement of the outer DNA layer, similar to that observed in Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II). Structural comparison with CtenDNAV-II revealed five key CP differences: the absence of surface-exposed C-terminal tails in ClorDNAV, the presence of a helical domain, differences in the projection domain conformation, variation in the number of β-strands in the jelly-roll fold, and the lack of ion-attributed densities at subunit interfaces. Together with the genome reconstruction, these findings underscore the importance of experimentally determined structures for understanding viral architecture and evolution. To complement these results, we analyzed AlphaFold3-predicted CPs from all classified Bacilladnaviridae genera. These models confirmed the conservation of the jelly-roll fold across the family while revealing variability in the surface-exposed and terminal regions, likely reflecting host-specific adaptations and genome packaging strategies. Together, the experimental and predicted structures provide a comprehensive view of structural conservation and divergence in Bacilladnaviridae. Furthermore, the results provide additional structural evidence for the evolution of ssDNA Bacilladnaviridae from a noda-like ssRNA virus ancestor and suggest a shared genome organization resembling that of double-stranded viruses.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein protein
B: Hypothetical protein protein
C: Hypothetical protein protein


Theoretical massNumber of molelcules
Total (without water)128,8403
Polymers128,8403
Non-polymers00
Water00
1
A: Hypothetical protein protein
B: Hypothetical protein protein
C: Hypothetical protein protein
x 60


Theoretical massNumber of molelcules
Total (without water)7,730,384180
Polymers7,730,384180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Hypothetical protein protein


Mass: 42946.578 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chaetoceros lorenzianus DNA virus / References: UniProt: E9RFF1
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: Chaetoceros lorenzianus DNA virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetoceros lorenzianus DNA virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Chaetoceros lorenzianus
Virus shellDiameter: 350 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 45.156 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 9352
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2EPU3.6.0image acquisition
4cryoSPARC4.5.3CTF correction
7Coot0.9.8.8model fitting
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8145 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038069
ELECTRON MICROSCOPYf_angle_d0.51710981
ELECTRON MICROSCOPYf_dihedral_angle_d5.3761092
ELECTRON MICROSCOPYf_chiral_restr0.0451202
ELECTRON MICROSCOPYf_plane_restr0.0051464

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