[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

TitleMolecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 10638, Year 2024
Publish dateDec 6, 2024
AuthorsXiaoyu Liu / Xian Xia / Michael W Martynowycz / Tamir Gonen / Z Hong Zhou /
PubMed AbstractVirus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ...Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., "molecular sociology") of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.
External linksNat Commun / PubMed:39639006 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution3.0 - 40.0 Å
Structure data

EMDB-46049, PDB-9cyt:
Cryo-EM structure of MRV outer shell
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-46053, PDB-9cyx:
Cryo-EM structure of MRV full core
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-46054, PDB-9cyy:
Cryo-EM structure of MRV virion
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-47313: Subtomogram averaging of MRV core from 6 h post infection
Method: EM (subtomogram averaging) / Resolution: 16.0 Å

EMDB-47314: Subtomogram averaging for MRV empty core from 6 h post infection
Method: EM (subtomogram averaging) / Resolution: 20.0 Å

EMDB-47315: Subtomogram averaging of MRV star core from cells 48 h post infection
Method: EM (subtomogram averaging) / Resolution: 14.0 Å

EMDB-47316: Subtomogram averaging of MRV virion from cells 48 h post infection
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

EMDB-47317: Subtomogram averaging of MRV virion vertex
Method: EM (subtomogram averaging) / Resolution: 6.9 Å

EMDB-47318: Subtomogram averaging of MRV empty virion from cells 48 h post infection
Method: EM (subtomogram averaging) / Resolution: 17.0 Å

EMDB-47319: Subtomogram averaging of MRV outer shell from cells 48 h post infection
Method: EM (subtomogram averaging) / Resolution: 40.0 Å

EMDB-47320: CryoEM structure of MRV empty virion 48 h post infection
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-47321: CryoEM structure of MRV empty core without turret attached
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-47322: CryoEM structure of MRV empty core with turret attached
Method: EM (single particle) / Resolution: 3.8 Å

Source
  • mammalian orthoreovirus 3 dearing
KeywordsVIRAL PROTEIN / Mammalian reovirus / outer shell

+
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