[English] 日本語
Yorodumi
- EMDB-48926: The Red Crowned-Crane Parvovirus Capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48926
TitleThe Red Crowned-Crane Parvovirus Capsid
Map data
Sample
  • Virus: Red-crowned crane parvovirus
    • Protein or peptide: Major capsid protein
  • Ligand: MAGNESIUM ION
KeywordsRCPV / Aveparvovirus / Parvovirus / capsid / VLP / cryo-EM / VIRUS
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesRed-crowned crane parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsHsi J / Mietzsch M / McKenna R
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-2236414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Virol / Year: 2025
Title: Birds of a feather flock together: structural characterization of red-crowned crane and turkey aveparvoviruses.
Authors: Jane Hsi / Mario Mietzsch / Matthew Patney / Sunny Chen / Anjelique Sawh-Gopal / Paul Chipman / Robert McKenna /
Abstract: 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 ...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.
History
DepositionFeb 4, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48926.png

Downloads & links

-
Map

FileDownload / File: emd_48926.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.72 Å/pix.
x 500 pix.
= 360. Å		0.72 Å/pix.
x 500 pix.
= 360. Å		0.72 Å/pix.
x 500 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.105829 - 13.939101000000001
Average (Standard dev.)-0.000000001928945 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_48926_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48926_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Red-crowned crane parvovirus

EntireName: Red-crowned crane parvovirus
Components
  • Virus: Red-crowned crane parvovirus
    • Protein or peptide: Major capsid protein
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Red-crowned crane parvovirus

SupramoleculeName: Red-crowned crane parvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2079601 / Sci species name: Red-crowned crane parvovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Red-crowned crane parvovirus
Molecular weightTheoretical: 58.906148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAADSSADA AVPMSDSPSG GGGGGGGGGI GESTGNWTCN TVWGKNSIIT NASRHCVCLT RDLDMYKAIG NKDNGLVFGT ENKTAWVGW STPWNYIDYN QMCVHFSPRD WQRLINTASK WRPRSVHIKI FNIQVIQKTT VSDGTQYSND LTGTIQIFAD A QGRYPKLL ...String:
MAAADSSADA AVPMSDSPSG GGGGGGGGGI GESTGNWTCN TVWGKNSIIT NASRHCVCLT RDLDMYKAIG NKDNGLVFGT ENKTAWVGW STPWNYIDYN QMCVHFSPRD WQRLINTASK WRPRSVHIKI FNIQVIQKTT VSDGTQYSND LTGTIQIFAD A QGRYPKLL YPCQTTMMGP FPNHIYYLPQ YAYTTACDGP TSNQDINALL NTNSAFYCLD ESPSAMLRTG NEWSCHYTFD DD TGWVHNT RSTIPIFERA NPLYDTWQVD LRGNDALRGH FSSWRQPWLP GPVINMTDGT AAGANLNTMP GVDVGASYMG IVP GPPICR AENDKDEYLQ TFWTPKTIGQ NEGDVKNSQI NTSTAYKSQV PTGRLWEVNA RGQYKAASSQ GNVADQQWAG CIPG MIWDR RPATYFDPIW QEKPITDDSF MYVSQMGGCT VSGAPGHIFV KNTPKPTGTA NEYVDEYSTF TITVTMEWEY EPHSF SQWN NYKMISNNES SAQAYVGMCN ASGQYVLNHS AGQLPEMWIT KNLSRVN

UniProtKB: Major capsid protein

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 120 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.47000000000000003 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 405850
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
About Yorodumi

-
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://pdbjlvh1.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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more