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- PDB-9nek: Capsid structure of the Syngnathus scovelli chapparvovirus virus-... -

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Basic information

Entry
Database: PDB / ID: 9nek
TitleCapsid structure of the Syngnathus scovelli chapparvovirus virus-like particle
ComponentsPutative structural protein VP
KeywordsVIRUS LIKE PARTICLE / parvovirus / fish virus / virus capsid / T=1 / icosahedral virus particle / chapparvovirus / chaphamaparvovirus
Function / homologyPutative structural protein VP
Function and homology information
Biological speciesSyngnathus scovelli chapparvovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsPenzes, J.J. / Kaelber, J.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Viruses / Year: 2025
Title: Capsid Structure of the Fish Pathogen Syngnathus Scovelli Chapparvovirus Offers a New Perspective on Parvovirus Structural Biology.
Authors: Judit J Penzes / Jason T Kaelber /
Abstract: Chapparvoviruses (ChPVs) comprise a divergent lineage of the ssDNA virus family and evolved to infect vertebrate animals independently from the subfamily. Despite being pathogenic and widespread in ...Chapparvoviruses (ChPVs) comprise a divergent lineage of the ssDNA virus family and evolved to infect vertebrate animals independently from the subfamily. Despite being pathogenic and widespread in environmental samples and metagenomic assemblies, their structural characterization has proven challenging. Here, we report the first structural analysis of a ChPV, represented by the fish pathogen, Syngnathus scovelli chapparvovirus (SsChPV). We show through the SsChPV structure that the lineage harbors a surface morphology, subunit structure, and multimer interactions that are unique among parvoviruses. The SsChPV capsid evolved a threefold-related depression of α-helices that is analogous to the β-annulus pore of denso- and hamaparvoviruses and may play a role in monomer oligomerization during assembly. As interacting β-strands are absent from the twofold symmetry axis, the viral particle lacks the typical stability and resilience of parvovirus capsids. Although all parvoviruses thus far rely on the threading of large, flexible N-terminal domains to the capsid surface for their intracellular trafficking, our results show that ChPVs completely lack any such N-terminal sequences. This led to the subsequent degradation of their fivefold channel, the site of N-terminus externalization. These findings suggest that ChPVs harbor an infectious pathway that significantly deviates from the rest of the .
History
DepositionFeb 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative structural protein VP


Theoretical massNumber of molelcules
Total (without water)41,9691
Polymers41,9691
Non-polymers00
Water00
1
A: Putative structural protein VP
x 60


Theoretical massNumber of molelcules
Total (without water)2,518,14960
Polymers2,518,14960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Putative structural protein VP


Mass: 41969.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gill tissue of male Syngnathus scovelli / Source: (gene. exp.) Syngnathus scovelli chapparvovirus / Details (production host): pFastBac1 / Cell line (production host): Sf9
Production host: Autographa californica nucleopolyhedrovirus
References: UniProt: A0A6B9D5B5
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: Syngnathus scovelli chapparvovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.41 MDa / Experimental value: YES
Source (natural)Organism: Syngnathus scovelli chapparvovirus
Source (recombinant)Organism: Autographa californica nucleopolyhedrovirus / Strain: AcNPV / Cell: Sf9 / Plasmid: pFastBac1
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Syngnathus scovelli
Virus shellName: virus particle / Diameter: 220 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.2
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Very diluted sample prep
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 K / Details: Front blotted only

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 31 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11910
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7Coot0.9.8.96model fitting
12cryoSPARC3D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14213
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2202 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 2.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417646
ELECTRON MICROSCOPYf_angle_d0.55424156
ELECTRON MICROSCOPYf_dihedral_angle_d4.9322274
ELECTRON MICROSCOPYf_chiral_restr0.0442598
ELECTRON MICROSCOPYf_plane_restr0.0053132

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