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- EMDB-12554: Bacilladnavirus capsid structure -

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Basic information

Entry
Database: EMDB / ID: EMD-12554
TitleBacilladnavirus capsid structure
Map dataCapsid map
Sample
  • Virus: Chaetoceros tenuissimus DNA virus type-II
    • Protein or peptide: Capsid protein VP2
Function / homologyUncharacterized protein
Function and homology information
Biological speciesChaetoceros tenuissimus DNA virus type-II
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMunke A / Okamoto K
Funding support Sweden, Japan, 2 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Japan Society for the Promotion of Science (JSPS)16H06429, 16K21723, 16H06437, and 19H00956 Japan
Citation
Journal: mBio / Year: 2022
Title: Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.
Authors: Anna Munke / Kei Kimura / Yuji Tomaru / Han Wang / Kazuhiro Yoshida / Seiya Mito / Yuki Hongo / Kenta Okamoto /
Abstract: Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on ...Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the single-stranded DNA (ssDNA) viruses from the family. We present the capsid structure of the bacilladnavirus DNA virus type II (CtenDNAV-II), determined at 2.4-Å resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold but has additional unique features; a third β-sheet and a long C-terminal tail. Furthermore, a low-resolution reconstruction of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organization. Single-stranded DNA (ssDNA) viruses are an extremely widespread group of viruses that infect diverse hosts from all three domains of life, consequently having great economic, medical, and ecological importance. In particular, bacilladnaviruses are highly abundant in marine sediments and greatly influence the dynamic appearance and disappearance of certain algae species. Despite the importance of ssDNA viruses and the last couple of years' advancements in cryo-electron microscopy, structural information on the genomes of ssDNA viruses remains limited. This paper describes two important achievements: (i) the first atomic structure of a bacilladnavirus capsid, which revealed that the capsid protein gene presumably was acquired from a ssRNA virus in early evolutionary events; and (ii) the structural organization of a ssDNA genome, which retains a spooled arrangement that previously only been observed for double-stranded viruses.
#1: Journal: mBio / Year: 2022
Title: Primordial capsid and spooled ssDNA genome structures reveal ancestral events of eukaryotic viruses
Authors: Munke A / Kimura K / Tomaru Y / Wang H / Yoshida K / Mito S / Yuki H / Okamoto K
History
DepositionMar 5, 2021-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12554.png

Downloads & links

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Map

FileDownload / File: emd_12554.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 450 pix.
= 477. Å		1.06 Å/pix.
x 450 pix.
= 477. Å		1.06 Å/pix.
x 450 pix.
= 477. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10912953 - 0.2825871
Average (Standard dev.)0.0015984548 (±0.011116781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 476.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_12554_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map sharpened by DeepEMhancer

Fileemd_12554_additional_1.map
AnnotationMap sharpened by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Capsid first half map

Fileemd_12554_half_map_1.map
AnnotationCapsid first half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Capsid second half map

Fileemd_12554_half_map_2.map
AnnotationCapsid second half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetoceros tenuissimus DNA virus type-II

EntireName: Chaetoceros tenuissimus DNA virus type-II
Components
  • Virus: Chaetoceros tenuissimus DNA virus type-II
    • Protein or peptide: Capsid protein VP2

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Supramolecule #1: Chaetoceros tenuissimus DNA virus type-II

SupramoleculeName: Chaetoceros tenuissimus DNA virus type-II / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Capsid / NCBI-ID: 1516127 / Sci species name: Chaetoceros tenuissimus DNA virus type-II / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chaetoceros tenuissimus (Diatom)
Virus shellShell ID: 1 / Diameter: 35.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros tenuissimus DNA virus type-II
Molecular weightTheoretical: 43.329559 KDa
SequenceString: MVRRRGGKTA GSKRPKMSSK NFGANRKRDF RRPARKSKAK KARSMAPAKT VRKSTTAGAH SKHFSVIGNP FSKATQQPQI PDGRMLESL PRRCQLVTEI RNNVTVGSNP TYILVAPSLG LAFQAYQDTN VPGGLDSSVY GLQNRGCTVR ANLSATSIEN Y NDIAKWRI ...String:
MVRRRGGKTA GSKRPKMSSK NFGANRKRDF RRPARKSKAK KARSMAPAKT VRKSTTAGAH SKHFSVIGNP FSKATQQPQI PDGRMLESL PRRCQLVTEI RNNVTVGSNP TYILVAPSLG LAFQAYQDTN VPGGLDSSVY GLQNRGCTVR ANLSATSIEN Y NDIAKWRI VSQGINLKLN NVEDENDGWY EACRFQHDWT PDELCLRSTE NDASTISQDE DLVMGVISSS FMNGALNTIG NN MVEQRGY ESGLLKNIHK RMFQLHNNTS AIRPKTLQGQ FNYGSEITFS GTESEARFTD VPSNRQLVDS LWHNDYDCIL IKL YPRENT GAAGQTGSAL IVNAIQNLEL QYSPTSDLST YHIANKRARM VEAKLDKKNN TDAAGEPFVP GSSR

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: Gctf (ver. 1.06), RELION (ver. 3.1))
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 33507
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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