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- PDB-7ns0: Bacilladnavirus capsid structure -

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Basic information

Entry
Database: PDB / ID: 7ns0
TitleBacilladnavirus capsid structure
ComponentsCapsid protein VP2
KeywordsVIRUS / Jelly-roll / capsid
Function / homologyUncharacterized protein
Function and homology information
Biological speciesChaetoceros tenuissimus DNA virus type-II
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMunke, A. / Okamoto, K.
Funding support Sweden, Japan, 2items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Capsid protein VP2
B2: Capsid protein VP2
C3: Capsid protein VP2


Theoretical massNumber of molelcules
Total (without water)129,9893
Polymers129,9893
Non-polymers00
Water00
1
A1: Capsid protein VP2
B2: Capsid protein VP2
C3: Capsid protein VP2
x 60


  • defined by author
  • Evidence: microscopy
  • 7.8 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)7,799,321180
Polymers7,799,321180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59

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Components

#1: Protein Capsid protein VP2


Mass: 43329.559 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus DNA virus type-II / References: UniProt: A0A0B6VL42

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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 tenuissimus DNA virus type-II / Type: VIRUS / Details: Capsid / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetoceros tenuissimus DNA virus type-II
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Chaetoceros tenuissimus
Virus shellDiameter: 35 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 37 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
5RELION3.1CTF correction
8Cootmodel fitting
10PHENIX1.18.2-3874model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33507 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 12.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00527216
ELECTRON MICROSCOPYf_angle_d0.7069800
ELECTRON MICROSCOPYf_chiral_restr0.0511090
ELECTRON MICROSCOPYf_plane_restr0.00481307
ELECTRON MICROSCOPYf_dihedral_angle_d15.2325984

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