[English] 日本語
Yorodumi
- EMDB-2523: Structure of the mammalian oligosaccharyl-transferase complex in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2523
TitleStructure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon
Map dataReconstruction was masked
Sample
  • Sample: Canis familiaris Sec61, OST and TRAP bound to a translocating wheat germ 80S ribosome
  • Complex: Triticum aestivum 80S ribosome
  • Protein or peptide: Sec61
  • Protein or peptide: Oligosaccharyltransferase
  • Protein or peptide: Translocon-Associated Protein omplex
KeywordsCo-translational protein translocation / N-Glycosylation
Biological speciesTriticum aestivum (bread wheat) / Canis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsPfeffer S / Dudek J / Gogala M / Schorr S / Linxweiler J / Lang S / Becker T / Beckmann R / Zimmermann F
CitationJournal: Nat Commun / Year: 2014
Title: Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon.
Authors: Stefan Pfeffer / Johanna Dudek / Marko Gogala / Stefan Schorr / Johannes Linxweiler / Sven Lang / Thomas Becker / Roland Beckmann / Richard Zimmermann / Friedrich Förster /
Abstract: In mammalian cells, proteins are typically translocated across the endoplasmic reticulum (ER) membrane in a co-translational mode by the ER protein translocon, comprising the protein-conducting ...In mammalian cells, proteins are typically translocated across the endoplasmic reticulum (ER) membrane in a co-translational mode by the ER protein translocon, comprising the protein-conducting channel Sec61 and additional complexes involved in nascent chain processing and translocation. As an integral component of the translocon, the oligosaccharyl-transferase complex (OST) catalyses co-translational N-glycosylation, one of the most common protein modifications in eukaryotic cells. Here we use cryoelectron tomography, cryoelectron microscopy single-particle analysis and small interfering RNA-mediated gene silencing to determine the overall structure, oligomeric state and position of OST in the native ER protein translocon of mammalian cells in unprecedented detail. The observed positioning of OST in close proximity to Sec61 provides a basis for understanding how protein translocation into the ER and glycosylation of nascent proteins are structurally coupled. The overall spatial organization of the native translocon, as determined here, serves as a reliable framework for further hypothesis-driven studies.
History
DepositionNov 26, 2013-
Header (metadata) releaseDec 18, 2013-
Map releaseJan 22, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2423.jpg

Downloads & links

-
Map

FileDownload / File: emd_2523.map.gz / Format: CCP4 / Size: 804.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction was masked
Voxel sizeX=Y=Z: 1.2374 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.41137141 - 0.9818064
Average (Standard dev.)0.00244991 (±0.03538019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-300-300-299
Dimensions600600600
Spacing600600600
CellA=B=C: 742.44006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23741.23741.2374
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z742.440742.440742.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-300-299
NX/NY/NZ600600600
MAP C/R/S213
start NC/NR/NS-300-300-299
NC/NR/NS600600600
D min/max/mean-0.4110.9820.002

-
Supplemental data

-
Sample components

-
Entire : Canis familiaris Sec61, OST and TRAP bound to a translocating whe...

EntireName: Canis familiaris Sec61, OST and TRAP bound to a translocating wheat germ 80S ribosome
Components
  • Sample: Canis familiaris Sec61, OST and TRAP bound to a translocating wheat germ 80S ribosome
  • Complex: Triticum aestivum 80S ribosome
  • Protein or peptide: Sec61
  • Protein or peptide: Oligosaccharyltransferase
  • Protein or peptide: Translocon-Associated Protein omplex

-
Supramolecule #1000: Canis familiaris Sec61, OST and TRAP bound to a translocating whe...

SupramoleculeName: Canis familiaris Sec61, OST and TRAP bound to a translocating wheat germ 80S ribosome
type: sample / ID: 1000
Oligomeric state: One 80S ribosome binds one Sec61, one OST and one TRAP
Number unique components: 4

-
Supramolecule #1: Triticum aestivum 80S ribosome

SupramoleculeName: Triticum aestivum 80S ribosome / type: complex / ID: 1 / Name.synonym: Wheat germ 80S ribosome / Details: Data-subset resulted from computational sorting / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum aestivum (bread wheat) / synonym: Wheat Germ

-
Macromolecule #1: Sec61

MacromoleculeName: Sec61 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog

-
Macromolecule #2: Oligosaccharyltransferase

MacromoleculeName: Oligosaccharyltransferase / type: protein_or_peptide / ID: 2 / Name.synonym: OST / Recombinant expression: No
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog

-
Macromolecule #3: Translocon-Associated Protein omplex

MacromoleculeName: Translocon-Associated Protein omplex / type: protein_or_peptide / ID: 3 / Name.synonym: TRAP / Recombinant expression: No
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Details: 30 mM Hepes/KOH 7.6, 10 mM Mg(OAc)2, 180 mM KOAC/HAc pH 7.6, 0.3 % Digitonin, 1 mM DTT
GridDetails: Quantifoil grids pre-coated with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 148721 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJul 17, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 6119 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: On 3D-volume (SPIDER)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: SPIDER, Signature, MAPPOS
Details: This datasubset resulted from computational sorting.
Number images used: 15705
DetailsThe particles were selected using SIGNATURE, classified using MAPPOS and processed with SPIDER

-
Atomic model buiding 1

Initial modelPDB ID:

2wwb

SoftwareName: Chimera, Coot, MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more