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- EMDB-28550: Acheta domesticus segmented densovirus, mature virion capsid structure -

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Basic information

Entry
Database: EMDB / ID: EMD-28550
TitleAcheta domesticus segmented densovirus, mature virion capsid structure
Map dataCapsid structure of the Acheta domesticus densovirus mature virion
Sample
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Acheta domesticus segmented densovirus major capsid protein
    • DNA: DNA (5'-D(P*AP*AP*TP*AP*A)-3')
Keywordsparvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / VIRUS-DNA complex
Biological speciesunclassified Densovirinae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsPenzes JJ / McKenna R / Tijssen P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
National Institutes of Health/Office of the DirectorOD018142 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR025080 United States
CitationJournal: Nat Commun / Year: 2023
Title: Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus.
Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Emmanuel W Smith / Robert McKenna / Peter Tijssen /
Abstract: Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression ...Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
History
DepositionOct 11, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28550.png

Downloads & links

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Map

FileDownload / File: emd_28550.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid structure of the Acheta domesticus densovirus mature virion
Voxel sizeX=Y=Z: 1.038 Å
Density
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-20.898102000000002 - 22.973001
Average (Standard dev.)0.000000000176855 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 467.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : unclassified Densovirinae

EntireName: unclassified Densovirinae (virus)
Components
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Acheta domesticus segmented densovirus major capsid protein
    • DNA: DNA (5'-D(P*AP*AP*TP*AP*A)-3')

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Supramolecule #1: unclassified Densovirinae

SupramoleculeName: unclassified Densovirinae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 185880 / Sci species name: unclassified Densovirinae / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acheta domesticus (house cricket)
Virus shellShell ID: 1 / Name: Acheta domesticus segmented densovirus capsid / Diameter: 210.0 Å / T number (triangulation number): 1

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Macromolecule #1: Acheta domesticus segmented densovirus major capsid protein

MacromoleculeName: Acheta domesticus segmented densovirus major capsid protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified Densovirinae (virus)
Molecular weightTheoretical: 37.793566 KDa
SequenceString: TKEGYGKHIT SMHVRNIFNQ GNQVIRNIVK QQRYELLDFT GTEAGTTNLP KIIPYQCIWW RGLQNAANVN QTINNMIALN TISYGVRFL KAKLCIEVYA VTRKRLIQTG ATSYYTDDFE QGQNLFIGWA DRKAESIPIT TPADLDETKL TVANTTLFDA N NDNITKEE ...String:
TKEGYGKHIT SMHVRNIFNQ GNQVIRNIVK QQRYELLDFT GTEAGTTNLP KIIPYQCIWW RGLQNAANVN QTINNMIALN TISYGVRFL KAKLCIEVYA VTRKRLIQTG ATSYYTDDFE QGQNLFIGWA DRKAESIPIT TPADLDETKL TVANTTLFDA N NDNITKEE VPTREKWCHT WDLDVLNHNY LWEPNNLDSQ WTLIPGAQAV QPTATPIGPT YQEIVIATKA IGANESALVT TI QDRRSYP RLMLSQPQIK DETDTMKFKY QIRISTELEM EHHIKPDIAN PWLTRQTLPL PALSGDGTTR YVPCVPYETH VSQ RNWNHV GEYL

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Macromolecule #2: DNA (5'-D(P*AP*AP*TP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*TP*AP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified Densovirinae (virus)
Molecular weightTheoretical: 39.820621 KDa
SequenceString: (DG)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N) (N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N) (N)(N)(N)(N)(N)(N) (N)(N)(N) ...String:
(DG)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N) (N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N) (N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N) (N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N) (N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N) (N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N) (N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (DG)(DA)(DA)(DT)(DA)(DA)

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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

Concentration2 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 x / Component - Name: Phosphate-buffered saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV
DetailsDeceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.65 µm
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1411 / Average electron dose: 75.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 188074
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio random model based on 100 boxed particles
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 30 / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cisTEM (ver. 1.0.0)
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 150469

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Atomic model buiding 1

Initial modelPDB ID:

3ux1


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8er8:
Acheta domesticus segmented densovirus, mature virion capsid structure

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