[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

TitleThe structure of the COPI coat determined within the cell.
Journal, issue, pagesElife, Vol. 6, Year 2017
Publish dateNov 17, 2017
AuthorsYury S Bykov / Miroslava Schaffer / Svetlana O Dodonova / Sahradha Albert / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / John Ag Briggs /
PubMed AbstractCOPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively ...COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with reconstitution systems using purified components. Previously we have determined a complete structural model of the reconstituted COPI coat (Dodonova et al., 2017). Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified cells. The native algal structure resembles the mammalian structure, but additionally reveals cargo bound beneath β'-COP. We find that all coat components disassemble simultaneously and relatively rapidly after budding. Structural analysis , maintaining Golgi topology, shows that vesicles change their size, membrane thickness, and cargo content as they progress from to , but the structure of the coat machinery remains constant.
External linksElife / PubMed:29148969 / PubMed Central
MethodsEM (subtomogram averaging) / EM (tomography)
Resolution20.0 - 33.0 Å
Structure data

EMDB-3968:
The in situ structure of the Chlamydomonas COPI coat: average of all data
Method: EM (subtomogram averaging) / Resolution: 20.0 Å

EMDB-3969:
The in situ structure of the Chlamydomonas COPI coat: average from buds
Method: EM (subtomogram averaging) / Resolution: 23.0 Å

EMDB-3970:
The in situ structure of the Chlamydomonas COPI coat: average from vesicles
Method: EM (subtomogram averaging) / Resolution: 23.0 Å

EMDB-3971:
The in situ structure of the Chlamydomonas COPI coat: average from the cis-Golgi region
Method: EM (subtomogram averaging) / Resolution: 24.0 Å

EMDB-3972:
The in situ structure of the Chlamydomonas COPI coat: average from the medial/trans-Golgi region
Method: EM (subtomogram averaging) / Resolution: 23.0 Å

EMDB-3973:
The in situ structure of the Chlamydomonas COPI coat: average from the trans-Golgi/TGN region
Method: EM (subtomogram averaging) / Resolution: 24.0 Å

EMDB-3974:
The in situ structure of the Chlamydomonas COPI coat linkage I
Method: EM (subtomogram averaging) / Resolution: 33.0 Å

EMDB-3975:
The in situ structure of the Chlamydomonas COPI coat linkage II
Method: EM (subtomogram averaging) / Resolution: 32.0 Å

EMDB-3976:
The in situ structure of the Chlamydomonas COPI coat linkage IV
Method: EM (subtomogram averaging) / Resolution: 32.0 Å

EMDB-3977:
Cryo-electron tomogram of the Chlamydomonas reinhardtii Golgi apparatus
Method: EM (tomography)

Source
  • Chlamydomonas reinhardtii (plant)

+
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