[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

TitleAssembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Journal, issue, pagesPLoS Pathog, Vol. 13, Issue 6, Page e1006377, Year 2017
Publish dateJun 2, 2017
AuthorsVidya Mangala Prasad / Thomas Klose / Michael G Rossmann /
PubMed AbstractViral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe ...Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.
External linksPLoS Pathog / PubMed:28575072 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution11.1 - 35.0 Å
Structure data

EMDB-8248: Subtomogram-averaged surface glycoprotein spike density of rubella virus
PDB-5khc: Structure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus
Method: EM (subtomogram averaging) / Resolution: 11.1 Å

EMDB-8249: Subtomogram-averaged map of a single rubella virus capsid unit
PDB-5khe: Fitted structure of rubella virus capsid protein
Method: EM (subtomogram averaging) / Resolution: 35.0 Å

EMDB-8250: Subtomogram-averaged map of a single rubella virus capsid unit
PDB-5khf: Fitted structure of rubella virus capsid protein
Method: EM (subtomogram averaging) / Resolution: 35.0 Å

EMDB-8251:
Subtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex
Method: EM (subtomogram averaging) / Resolution: 35.0 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • rubella virus
  • Rubella virus strain M33
KeywordsVIRAL PROTEIN / Rubella virus / surface glycoprotein spike / E1-E2 heterodimer / rubella virus capsid protein

+
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