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- EMDB-49314: Capsid structure of the Syngnathus scovelli chapparvovirus virus-... -

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Basic information

Entry
Database: EMDB / ID: EMD-49314
TitleCapsid structure of the Syngnathus scovelli chapparvovirus virus-like particle
Map data
Sample
  • Virus: Syngnathus scovelli chapparvovirus
    • Protein or peptide: Putative structural protein VP
Keywordsparvovirus / fish virus / virus capsid / T=1 / icosahedral virus particle / chapparvovirus / chaphamaparvovirus / VIRUS LIKE PARTICLE
Function / homologyPutative structural protein VP
Function and homology information
Biological speciesSyngnathus scovelli chapparvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsPenzes JJ / Kaelber JT
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49314.png

Downloads & links

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Map

FileDownload / File: emd_49314.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 480 pix.
= 485.28 Å		1.01 Å/pix.
x 480 pix.
= 485.28 Å		1.01 Å/pix.
x 480 pix.
= 485.28 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.011 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.341
Minimum - Maximum-1.2880522 - 2.5816836
Average (Standard dev.)0.0014156316 (±0.121427335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 485.28003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-sharpened final map

Fileemd_49314_additional_1.map
AnnotationNon-sharpened final map
Projections & Slices
AxesZYX

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Half map: Half Map A

Fileemd_49314_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49314_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : Syngnathus scovelli chapparvovirus

EntireName: Syngnathus scovelli chapparvovirus
Components
  • Virus: Syngnathus scovelli chapparvovirus
    • Protein or peptide: Putative structural protein VP

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Supramolecule #1: Syngnathus scovelli chapparvovirus

SupramoleculeName: Syngnathus scovelli chapparvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2662396 / Sci species name: Syngnathus scovelli chapparvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Syngnathus scovelli (Gulf pipefish)
Molecular weightTheoretical: 410 KDa
Virus shellShell ID: 1 / Name: virus particle / Diameter: 220.0 Å / T number (triangulation number): 1

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Macromolecule #1: Putative structural protein VP

MacromoleculeName: Putative structural protein VP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Syngnathus scovelli chapparvovirus
Molecular weightTheoretical: 41.969145 KDa
Recombinant expressionOrganism: Autographa californica nucleopolyhedrovirus
SequenceString: MKFSNSYYAY IENQKNDYPD IGLERNPSEY QTGYHRIPNQ YWASFLTPKD WFNLIYNNKA FRVVGARCTV SNMIPLTEQA AIQGNTTIT TFNNTIYALC YTDNNYETEW EEPAARDLSF MWREGLTNGA RHMLPTYKHG IYRTTTSQAH NVFYGWDPLC K AENILELR ...String:
MKFSNSYYAY IENQKNDYPD IGLERNPSEY QTGYHRIPNQ YWASFLTPKD WFNLIYNNKA FRVVGARCTV SNMIPLTEQA AIQGNTTIT TFNNTIYALC YTDNNYETEW EEPAARDLSF MWREGLTNGA RHMLPTYKHG IYRTTTSQAH NVFYGWDPLC K AENILELR PGKNAVTFEW HAKEEIWLNT HMMQQFDPTH TPGIANTATV YSQEIHNQTH SNVTPHSHLN RWISQTDTAP AT ARHWSKQ AIQRPGIMEQ QFRYPIPNWF IKMIPLFDSQ NNLIKTTAQV LITMELTVDT IPQSLAINMP IIDDIIAPNH TPN SVPYCM FRYQPIIPIN VGVLPAPPTK GVFIPELPAR SDPTSDVE

UniProtKB: Putative structural protein VP

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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

Concentration0.05 mg/mL
BufferpH: 7.2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 297 K / Instrument: LEICA EM GP / Details: Front blotted only.
DetailsVery diluted sample prep

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Electron microscopy

MicroscopeTFS TALOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 11910 / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 14213
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model reconstruction
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2202
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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