[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

TitleInsights into the spool-like architecture and infection strategy of an enveloped archaeal virus.
Journal, issue, pagesSci Adv, Vol. 11, Issue 29, Page eadv7326, Year 2025
Publish dateJul 18, 2025
AuthorsHaonan Zhang / Haina Wang / Yan Li / Yunxuan Fan / Zhenfeng Zhang / Hongyu Chen / Kai Song / Li Huang / Ping Zhu /
PubMed AbstractArchaeal viruses are well known for their diverse morphologies and extreme stability. Here, we used cryo-electron tomography to analyze the structure of ellipsoid virus 1 (SEV1), an archaeal virus ...Archaeal viruses are well known for their diverse morphologies and extreme stability. Here, we used cryo-electron tomography to analyze the structure of ellipsoid virus 1 (SEV1), an archaeal virus with an ellipsoidal shape and a lipid envelope, and its infection strategy. We show that the SEV1 nucleocapsid adopts a "coil-stacking" architecture with substantial flexibility. The major capsid protein VP4, whose homologs are widespread in the thermoacidic environments around the Pacific Rim, binds genomic DNA in the formation of a nucleoprotein filament with a "beads-on-a-string" appearance. The virion is notably stable at high temperature and acidic pH, and the envelope of SEV1 is crucial to the thermostability of the virion. The infected cell undergoes cytoplasmic condensation to form patches associated with the assembly intermediates of the progeny virions. The nascent virions are released through virus-associated pyramids (VAPs), which are constructed of an SEV1 protein distinctly different at the amino acid sequence level from other known VAP proteins.
External linksSci Adv / PubMed:40680112 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution18.1 - 40.8 Å
Structure data

EMDB-62178: The average map of six beads composed of the nucleocapsid protein from SEV1
Method: EM (subtomogram averaging) / Resolution: 18.1 Å

EMDB-62341: The average map of eighteen beads composed of the NP from SEV1.
Method: EM (subtomogram averaging) / Resolution: 21.1 Å

EMDB-62342: The DNA coil forming by the nucleoprotein filaments in SEV1
Method: EM (subtomogram averaging) / Resolution: 24.7 Å

EMDB-62348: The lattice-like arrangement of nucleocapsid beads in SEV1
Method: EM (subtomogram averaging) / Resolution: 36.2 Å

EMDB-62349: The averaged map of pronounced stacking discs with a conspicuous channel
Method: EM (subtomogram averaging) / Resolution: 40.8 Å

+
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