[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

TitleStructural insights into scaffold-guided assembly of the Pseudomonas phage D3 capsid.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 11586, Year 2025
Publish dateNov 23, 2025
AuthorsAnna K Belford / Joshua B Maurer / Robert L Duda / Alexis Huet / James F Conway /
PubMed AbstractTailed bacteriophages comprise the largest structural family of viruses with close relatives in archaea and the eukaryotic herpesviruses. The common assembly pathway produces an icosahedrally ...Tailed bacteriophages comprise the largest structural family of viruses with close relatives in archaea and the eukaryotic herpesviruses. The common assembly pathway produces an icosahedrally symmetric protein shell, called capsid, into which the double-stranded DNA genome is packaged. While capsid sizes and amino acid sequences vary considerably, the major capsid protein (MCP) folds are remarkably similar throughout the family. To investigate the mechanisms governing capsid size, we characterize the procapsid and mature capsid of phage D3, which expresses an icosahedral lattice with Triangulation number T = 9. We find that the MCP scaffold domain binds to the interior capsid surface, acting as a clamp to constrain subunit interactions. Following scaffold digestion, the MCP capsid domains form strong interactions that maintain capsid structure throughout maturation. The scaffold constraints appear critical for capsid size determination and provide important understanding of the factors governing capsid assembly in general and expands our understanding of these ecologically and biomedically important viruses.
External linksNat Commun / PubMed:41274907 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.7 Å
Structure data

70800

9osb

EMDB-70800: D3 prohead 1 - icosahedral reconstruction
PDB-9osb: D3 prohead 1
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-70831: Penton focused prohead 1
Method: EM (single particle) / Resolution: 3.2 Å

70832

9oth

EMDB-70832, PDB-9oth:
D3 prohead 1
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-70834: Penton focused D3 prohead 2
Method: EM (single particle) / Resolution: 3.5 Å

70878

9ous

EMDB-70878, PDB-9ous:
D3 Virion icos
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-70879: Penton focused D3 virion capsid
Method: EM (single particle) / Resolution: 2.7 Å

70884

9ouz

EMDB-70884, PDB-9ouz:
Icosahedral D3 expanded capsid
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-70887: Penton focused expanded D3 capsid
Method: EM (single particle) / Resolution: 3.5 Å

Source
  • pseudomonas phage d3 (virus)
KeywordsVIRUS LIKE PARTICLE / Icosahedral symmetry / bacteriophage / procapsid / capsid / HK97 fold / VIRUS / C5 symmetry

+
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