[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleBirds of a feather flock together: structural characterization of red-crowned crane and turkey aveparvoviruses.
Journal, issue, pagesJ Virol, Vol. 99, Issue 7, Page e0011025, Year 2025
Publish dateJul 22, 2025
AuthorsJane Hsi / Mario Mietzsch / Matthew Patney / Sunny Chen / Anjelique Sawh-Gopal / Paul Chipman / Robert McKenna /
PubMed AbstractThe parvoviruses have non-enveloped = 1 icosahedral capsids that are ~25 nm in diameter, which package linear single-stranded DNA and infect a wide range of hosts. To date, parvoviruses affecting ...The parvoviruses have non-enveloped = 1 icosahedral capsids that are ~25 nm in diameter, which package linear single-stranded DNA and infect a wide range of hosts. To date, parvoviruses affecting birds have been identified in two genera: - and , and no capsid structures have been determined for any member of . This study investigates two bird viruses of this genus: red-crowned crane parvovirus (RCPV) and turkey parvovirus (TuPV). While the pathogenicity of RCPV is currently unknown, TuPV has been associated with gastrointestinal diseases, especially in juvenile birds. High-resolution structures of the RCPV and TuPV capsids were determined by cryo-electron microscopy at a resolution of 2.66 Å and 2.35 Å, respectively. A structural comparison of the RCPV and TuPV capsids shows that they exhibit many conserved features, such as a channel at the five-fold symmetry axis and surface depressions at the two-fold axis, as previously observed in parvoviruses from other genera. However, major structural differences were observed at the three-fold axes, with both RCPV and TuPV displaying recessed protrusions. In addition, terminal sialic acid was identified as a potential glycan receptor for RCPV. This study extends the architectural portfolio of structural parvovirology and will provide insights into parvoviral diversity and characterization of these viruses.IMPORTANCEThis study presents the capsid structures of two aveparvoviruses, red-crowned crane parvovirus (RCPV) and turkey parvovirus (TuPV), extending the structural repertoire of the . While the pathogenicity of RCPV is unknown, the red-crowned cranes are among the rarest crane species. To date, very few virological studies have been conducted for this rare avian species, and understanding their virome could contribute to conservation efforts. Additionally, several studies have previously suggested that TuPV is associated with cases of enteric disease syndrome. To date, no commercial antivirals or vaccines are available for TuPV. The structural characterization of its capsid may contribute toward the development of a treatment to control the spread of infection.
External linksJ Virol / PubMed:40607800 / PubMed Central
MethodsEM (single particle)
Resolution2.35 - 2.66 Å
Structure data

EMDB-48926, PDB-9n5l:
The Red Crowned-Crane Parvovirus Capsid
Method: EM (single particle) / Resolution: 2.66 Å

EMDB-48927, PDB-9n5m:
The Turkey Parvovirus Capsid structure
Method: EM (single particle) / Resolution: 2.35 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • red-crowned crane parvovirus
  • turkey parvovirus 260
KeywordsVIRUS / RCPV / Aveparvovirus / Parvovirus / capsid / VLP / cryo-EM / Turkey Parvovirus / TuPV

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more