[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

TitleStructural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.
Journal, issue, pagesScience, Vol. 360, Issue 6385, Page 215-219, Year 2018
Publish dateApr 13, 2018
AuthorsKatharina Braunger / Stefan Pfeffer / Shiteshu Shrimal / Reid Gilmore / Otto Berninghausen / Elisabet C Mandon / Thomas Becker / Friedrich Förster / Roland Beckmann /
PubMed AbstractProtein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and ...Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.
External linksScience / PubMed:29519914 / PubMed Central
MethodsEM (subtomogram averaging) / EM (single particle)
Resolution4.2 - 30.0 Å
Structure data

EMDB-4306:
Subtomogram average of unsorted ribosome-translocon complexes from STT3B(-/-) HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4307:
Subtomogram average of OST-free ribosome-translocon complexes from STT3B(-/-) HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4308:
Subtomogram average of OST-containing ribosome-translocon complexes from STT3B(-/-) HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4309:
Subtomogram average of unsorted ribosome-translocon complexes from STT3A(-/-) HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4310:
Subtomogram average of OST-free ribosome-translocon complexes from STT3A(-/-) HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4311:
Subtomogram average of ribosome-translocon complexes from STT3A(-/-) HEK cells containing an unidentified ER-lumenal component
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4312:
Subtomogram average of unsorted ribosome-translocon complexes from wild type HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4313:
Subtomogram average of OST-free ribosome-translocon complexes from wild type HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4314:
Subtomogram average of OST-containing ribosome-translocon complexes from wild type HEK cells
Method: EM (subtomogram averaging) / Resolution: 30.0 Å

EMDB-4315, PDB-6ftg:
Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes
Method: EM (subtomogram averaging) / Resolution: 9.1 Å

EMDB-4316, PDB-6fti:
Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-4317, PDB-6ftj:
Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome
Method: EM (single particle) / Resolution: 4.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-9UB:
[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid

Source
  • Homo sapiens (human)
  • canis lupus familiaris (dog)
  • oryctolagus cuniculus (rabbit)
  • Rabbit (rabbit)
  • Dog (dog)
KeywordsPROTEIN TRANSPORT / Protein translocon of the endoplasmic reticulum

+
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