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- EMDB-54550: Capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV),... -

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Basic information

Entry
Database: EMDB / ID: EMD-54550
TitleCapsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV), a CRESS-DNA bacilladnavirus
Map data
Sample
  • Virus: Chaetoceros lorenzianus DNA virus
    • Protein or peptide: Hypothetical protein protein
KeywordsCRESS-DNA virus / Cressdnaviricota / Bacilladnaviridae / ClorDNAV / capsid structure / single-stranded DNA virus / jelly-roll / structural virology / virus evolution / VIRUS
Function / homologyShotokuvirus capsid protein / Hypothetical protein protein
Function and homology information
Biological speciesChaetoceros lorenzianus DNA virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsMunke A / Gebhard J
Funding support Sweden, 1 items
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, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54550.png

Downloads & links

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Map

FileDownload / File: emd_54550.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 672 pix.
= 554.4 Å		0.83 Å/pix.
x 672 pix.
= 554.4 Å		0.83 Å/pix.
x 672 pix.
= 554.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.23195599 - 0.5762756
Average (Standard dev.)0.0019905434 (±0.03429359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 554.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54550_msk_1.map
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Additional map: Sharpened map

Fileemd_54550_additional_1.map
AnnotationSharpened map
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Half map: #2

Fileemd_54550_half_map_1.map
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Half map: #1

Fileemd_54550_half_map_2.map
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Sample components

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Entire : Chaetoceros lorenzianus DNA virus

EntireName: Chaetoceros lorenzianus DNA virus
Components
  • Virus: Chaetoceros lorenzianus DNA virus
    • Protein or peptide: Hypothetical protein protein

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Supramolecule #1: Chaetoceros lorenzianus DNA virus

SupramoleculeName: Chaetoceros lorenzianus DNA virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 754441 / Sci species name: Chaetoceros lorenzianus DNA virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chaetoceros lorenzianus (Diatom)
Virus shellShell ID: 1 / Diameter: 350.0 Å / T number (triangulation number): 3

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Macromolecule #1: Hypothetical protein protein

MacromoleculeName: Hypothetical protein protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros lorenzianus DNA virus
Molecular weightTheoretical: 42.946578 KDa
SequenceString: MAGRRKQRRS RAPRRKRTTG RKTLKRKADS RATPAKSTRK RTKTVSGAAK HHAVRVKPFS NATTQPKIPD GLLTSSLSRR LQNVVGVRN GNSPSVHAGS DVMHVVIAPT LGVPVMIANS AEGVLKRPGL SQESSFIGFP GQTVGFENLI ESTGVPTWPP T IPTGQKLE ...String:
MAGRRKQRRS RAPRRKRTTG RKTLKRKADS RATPAKSTRK RTKTVSGAAK HHAVRVKPFS NATTQPKIPD GLLTSSLSRR LQNVVGVRN GNSPSVHAGS DVMHVVIAPT LGVPVMIANS AEGVLKRPGL SQESSFIGFP GQTVGFENLI ESTGVPTWPP T IPTGQKLE NKGGFVLWRI ISQGLRIDLA NSDEENDGWF EACRFNWRNV PRDVCMTPLD GSTTTNSIGI APNPLWLEEV GY GMAMVEQ PGYKSGLLKD IKKAEFMLHP RTTTHDPTLI DPFEYGGSMT SSGGIDNVYY PSDNVSGNAV RFRDMGVDQN MDW IYIRLH CRPNNGTSSL GSNFLFNVIQ NVEVAFNPSS DFAAFQTINK ADTKTKMVAD GLNNNPDVFN GRRK

UniProtKB: Hypothetical protein 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

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9352 / Average exposure time: 2.4 sec. / Average electron dose: 45.156 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 8145
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

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

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