[English] 日本語
Yorodumi
- EMDB-1528: Single copies of Sec61 and TRAP associate with a nontranslating m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1528
TitleSingle copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome
Map dataThis is an average volume from 101000 aligned mammalian ribosome-channel complexes.
Sample
  • Sample: Mammalian native ribosome-channel complex
  • Complex: ribosome channel complex
Keywordscryo electron microscopy / single particle analysis / ribosome / Sec61 channel / TRAP / ER membrane. co-translational protein translocation
Function / homology
Function and homology information


intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane
Similarity search - Function
Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. ...Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
Preprotein translocase subunit SecG / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsMenetret JF / Hegde RS / Aguiar M / Gygi SP / Park E / Rapoport TA / Akey CW
CitationJournal: Structure / Year: 2008
Title: Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
Authors: Jean-François Ménétret / Ramanujan S Hegde / Mike Aguiar / Steven P Gygi / Eunyong Park / Tom A Rapoport / Christopher W Akey /
Abstract: During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we ...During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.
History
DepositionJun 23, 2008-
Header (metadata) releaseJun 24, 2008-
Map releaseApr 15, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3dkn
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3dkn
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD1528_Ribi...

Downloads & links

-
Map

FileDownload / File: emd_1528.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an average volume from 101000 aligned mammalian ribosome-channel complexes.
Voxel sizeX=Y=Z: 2.73 Å
Density
Contour Level1: 1.0 / Movie #1: 2
Minimum - Maximum-16.948399999999999 - 24.330400000000001
Average (Standard dev.)0.223987 (±1.52834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 458.64 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z458.640458.640458.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-16.94824.3300.224

-
Supplemental data

-
Sample components

-
Entire : Mammalian native ribosome-channel complex

EntireName: Mammalian native ribosome-channel complex
Components
  • Sample: Mammalian native ribosome-channel complex
  • Complex: ribosome channel complex

-
Supramolecule #1000: Mammalian native ribosome-channel complex

SupramoleculeName: Mammalian native ribosome-channel complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightTheoretical: 3.77 MDa / Method: from primary sequence

-
Supramolecule #1: ribosome channel complex

SupramoleculeName: ribosome channel complex / type: complex / ID: 1 / Name.synonym: ribosome-channel complex
Details: Sample solubilized from ER membranes with digitonin.
Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog
Molecular weightTheoretical: 3.77 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 30mM Hepes 50mM KAc, 10mM Mg acetate and 1.5% digitonin.
GridDetails: 400 mesh Cu grids with thin continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 111 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: home-made plunger. in cold room
Method: 1 second blot

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: single tilt / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: corrected on-axis at 150K mag
Detailsdata were collected on Oxford and Gatan cryo-holders
DateJul 27, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.54 µm / Number real images: 500 / Average electron dose: 15 e/Å2 / Details: Creoscitex Eversmart was used to scan negatives. / Od range: 1 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: per micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 79000
Details101000 particles were selected using boxer (of EMAN) used as semi-automatic selection program

-
Atomic model buiding 1

Initial model(PDB ID:

2zkr
PDB Unreleased entry

,

1rhz

,

2brd

)
SoftwareName: Chimera (UCSF)
DetailsProtocol: rigid body and manual fitting. The PDBs were fitted using Chimera. The ribosome binding loops of 1RHZ were then flexibly fitted into the riboeome and the stereochemistry was regularized with Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3dkn:
Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum

+
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