[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

TitleVESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly.
Journal, issue, pagesScience, Vol. 349, Issue 6244, Page 195-198, Year 2015
Publish dateJul 10, 2015
AuthorsS O Dodonova / P Diestelkoetter-Bachert / A von Appen / W J H Hagen / R Beck / M Beck / F Wieland / J A G Briggs /
PubMed AbstractTransport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats ...Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo-electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum. The highly interconnected COPI coat structure contradicted the current "adaptor-and-cage" understanding of coated vesicle formation.
External linksScience / PubMed:26160949
MethodsEM (subtomogram averaging) / EM (tomography)
Resolution13.0 - 23.0 Å
Structure data

2985

5a1u

EMDB-2985, PDB-5a1u:
The structure of the COPI coat triad
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

2986

5a1v

EMDB-2986, PDB-5a1v:
The structure of the COPI coat linkage I
Method: EM (subtomogram averaging) / Resolution: 21.0 Å

2987

5a1w

EMDB-2987, PDB-5a1w:
The structure of the COPI coat linkage II
Method: EM (subtomogram averaging) / Resolution: 18.0 Å

2988

5a1x

EMDB-2988, PDB-5a1x:
The structure of the COPI coat linkage III
Method: EM (subtomogram averaging) / Resolution: 23.0 Å

2989

5a1y

EMDB-2989, PDB-5a1y:
The structure of the COPI coat linkage IV
Method: EM (subtomogram averaging) / Resolution: 21.0 Å

Source
  • mus musculus (house mouse)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSPORT PROTEIN / STRUCTURAL PROTEIN / COPI / COATOMER / COATED VESICLES

+
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