9NEK | pdb_00009nek

Capsid structure of the Syngnathus scovelli chapparvovirus virus-like particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Capsid Structure of the Fish Pathogen Syngnathus Scovelli Chapparvovirus Offers a New Perspective on Parvovirus Structural Biology.

Penzes, J.J.Kaelber, J.T.

(2025) Viruses 17

  • DOI: https://doi.org/10.3390/v17050679
  • Primary Citation of Related Structures:  
    9NEK

  • PubMed Abstract: 

    Chapparvoviruses (ChPVs) comprise a divergent lineage of the Parvoviridae ssDNA virus family and evolved to infect vertebrate animals independently from the Parvovirinae 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 Parvoviridae .


  • Organizational Affiliation
    • Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08812, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative structural protein VP364Syngnathus scovelli chapparvovirusMutation(s): 0 
UniProt
Find proteins for A0A6B9D5B5 (Syngnathus scovelli chapparvovirus)
Explore A0A6B9D5B5 
Go to UniProtKB:  A0A6B9D5B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6B9D5B5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Database references