[English] 日本語
Yorodumi
- EMDB-2646: Structure of the mammalian ribosome-Sec61 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2646
TitleStructure of the mammalian ribosome-Sec61 complex
Map dataMammalian ribosome in complex with Sec61. Class with eEF2
Sample
  • Sample: Mammalian ribosome in complex with Sec61 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


TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / 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 ...TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / 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) / : / multicellular organism development / protein tyrosine kinase inhibitor activity / translation at presynapse / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / alpha-beta T cell differentiation / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / organelle membrane / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / translation regulator activity / cytosolic ribosome / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / SH2 domain binding / cyclin binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of GTPase activity / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of translation / cellular response to glucose stimulus / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / positive regulation of protein-containing complex assembly / negative regulation of cell growth / cellular response to gamma radiation / receptor tyrosine kinase binding / cellular response to growth factor stimulus / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / rRNA processing / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / regulation of protein localization / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome biogenesis / presynapse / ribosome binding / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / heparin binding / ribosomal small subunit assembly / small ribosomal subunit / midbody / 5S rRNA binding / large ribosomal subunit rRNA binding / perikaryon / protein phosphatase binding
Similarity search - Function
: / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...: / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e 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 S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e signature 2. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein L30e, conserved site / Ribosomal protein S7e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S23, eukaryotic/archaeal / 60S ribosomal protein L19 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature.
Similarity search - Domain/homology
Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / 40S ribosomal protein S19 / Uncharacterized protein / 40S ribosomal protein S4 / Large ribosomal subunit protein eL21 / S10_plectin domain-containing protein ...Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / 40S ribosomal protein S19 / Uncharacterized protein / 40S ribosomal protein S4 / Large ribosomal subunit protein eL21 / S10_plectin domain-containing protein / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL20 / 40S ribosomal protein S11 / Ribosomal protein L23/L25 N-terminal domain-containing protein / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34 / Ribosomal protein S5 / 40S ribosomal protein S8 / : / Uncharacterized protein / 40S ribosomal protein S27a / 40S ribosomal protein S7 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL24 / Ribosomal protein L15 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L13 / : / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / 60S ribosomal protein L12 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL18
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 13, 2014-
Header (metadata) releaseJun 18, 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: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j7p
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2646.png

Downloads & links

-
Map

FileDownload / File: emd_2646.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian ribosome in complex with Sec61. Class with eEF2
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.58023405 - 0.91271955
Average (Standard dev.)0.00144487 (±0.02510119)
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-0.5800.9130.001

-
Supplemental data

-
Supplemental map: emd 2646 half map 1.map

Fileemd_2646_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 2646 half map 2.map

Fileemd_2646_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 with the large subunit (...

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

-
Supramolecule #1000: Mammalian ribosome in complex with Sec61 with the large subunit (...

SupramoleculeName: Mammalian ribosome in complex with Sec61 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: 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: 3.5 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://pdbjlvh1.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