[English] 日本語
Yorodumi
- EMDB-2650: Structure of the mammalian ribosome-Sec61 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2650
TitleStructure of the mammalian ribosome-Sec61 complex
Map dataFinal map for mammalian ribosome in complex with Sec61 in idle configuration with the large subunit masked along refinement
Sample
  • Sample: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
  • Complex: Mammalian ribosome
  • Protein or peptide: Sec61
Keywordstranslation / ribosome / mammalian / sec61
Function / homology
Function and homology information


regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / : / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / : / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-transporting ATPase activity / translation at presynapse / embryonic brain development / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / organelle membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein localization to nucleus / protein targeting / protein-RNA complex assembly / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / translation regulator activity / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / innate immune response in mucosa / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / protein tag activity / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / protein transport / antibacterial humoral response / regulation of translation / heparin binding / presynapse / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / postsynaptic density / protein stabilization / rRNA binding / defense response to Gram-positive bacterium / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / glutamatergic synapse / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / extracellular space / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit ...: / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / 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 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L14e domain / Ribosomal protein L35Ae, conserved site / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L35Ae signature. / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic
Similarity search - Domain/homology
Ribosomal protein L15 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Protein transport protein Sec61 subunit alpha isoform 1 / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L36a ...Ribosomal protein L15 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Protein transport protein Sec61 subunit alpha isoform 1 / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L36a / 60S ribosomal protein L8 / 60S ribosomal protein L36 / Ribosomal protein L37 / Ribosomal protein L19 / 60S ribosomal protein L23 / 60S ribosomal protein L7 / Protein transport protein Sec61 subunit gamma / 60S ribosomal protein L37a / 60S ribosomal protein L28 isoform 2 / 60S ribosomal protein L13a isoform 1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L13 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL39 / Ribosomal protein L18 / 60S ribosomal protein L7a / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL29
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVoorhees RM / Fernandez IS / Scheres SHW / Hegde R
CitationJournal: Cell / Year: 2014
Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde /
Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
History
DepositionMay 14, 2014-
Header (metadata) releaseMay 28, 2014-
Map releaseJul 16, 2014-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j7q
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2650.png

Downloads & links

-
Map

FileDownload / File: emd_2650.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map for mammalian ribosome in complex with Sec61 in idle configuration with the large subunit masked along refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å		1.34 Å/pix.
x 420 pix.
= 562.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.59921467 - 1.04274726
Average (Standard dev.)0.00135073 (±0.02352491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 562.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z562.800562.800562.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.5991.0430.001

-
Supplemental data

-
Supplemental map: emd 2650 half map 1.map

Fileemd_2650_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 2650 half map 2.map

Fileemd_2650_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mammalian ribosome in complex with Sec61 in a idle configuration ...

EntireName: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
Components
  • Sample: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
  • Complex: Mammalian ribosome
  • Protein or peptide: Sec61

-
Supramolecule #1000: Mammalian ribosome in complex with Sec61 in a idle configuration ...

SupramoleculeName: Mammalian ribosome in complex with Sec61 in a idle configuration with the large subunit (60S) masked during processing.
type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Mammalian ribosome

SupramoleculeName: Mammalian ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: Domestic Pig / Tissue: pancreas

-
Macromolecule #1: Sec61

MacromoleculeName: Sec61 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / synonym: Domestic Pig

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 50mM HEPES, 200mM K-acetate, 15mM Mg-acetate, 1mM DTT
GridDetails: Quantifoil R2/2 400 mesh copper grids.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV
Method: 3uL of sampled was incubated on the grid for 30 seconds before blotting for 9 second

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateApr 7, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1900 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80019

+
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