[English] 日本語
Yorodumi
- EMDB-2644: Structure of the mammalian ribosome-Sec61 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2644
TitleStructure of the mammalian ribosome-Sec61 complex
Map dataMammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs
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


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / : / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RMTs methylate histone arginines / Protein methylation / TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / : / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / VLDLR internalisation and degradation / Interferon alpha/beta signaling / Negative regulators of DDX58/IFIH1 signaling / RAS processing / Inactivation of CSF3 (G-CSF) signaling / Regulation of BACH1 activity / KEAP1-NFE2L2 pathway / Regulation of NF-kappa B signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / regulation of cell cycle => GO:0051726 / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Stimuli-sensing channels / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / ABC-family proteins mediated transport / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Ub-specific processing proteases / Ovarian tumor domain proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin D associated events in G1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
: / : / Malate dehydrogenase, type 3 / 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. ...: / : / Malate dehydrogenase, type 3 / 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 / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S12e / : / Small (40S) ribosomal subunit Asc1/RACK1 / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / : / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein L1
Similarity search - Domain/homology
Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S27 / 40S ribosomal protein S6 / 40S ribosomal protein S10 / 40S ribosomal protein S15a ...Ribosomal protein L15 / 40S ribosomal protein S7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / 40S ribosomal protein S27 / 40S ribosomal protein S6 / 40S ribosomal protein S10 / 40S ribosomal protein S15a / 60S ribosomal protein L35a / 60S ribosomal protein L23a / 60S ribosomal protein L3 isoform a / 60S ribosomal protein L13a isoform 1 / 60S ribosomal protein L36a / Ribosomal protein / 60S ribosomal protein L8 / 40S ribosomal protein S9 isoform a / 60S ribosomal protein L36 / 40S ribosomal protein S11 / Ribosomal protein L37 / 40S ribosomal protein S25 / Ribosomal protein L19 / 60S ribosomal protein L23 / 60S ribosomal protein L7 / 40S ribosomal protein S30 / Protein transport protein Sec61 subunit gamma / 60S ribosomal protein L37a / Malate dehydrogenase / 60S ribosomal protein L28 isoform 2 / 40S ribosomal protein S19 / Large ribosomal subunit protein eL24 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L13 / Plug_translocon domain-containing protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL39 / 40S ribosomal protein S4 / Ribosomal protein L18 / 40S ribosomal protein S27a / 60S ribosomal protein L7a / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Ribosomal protein S5 / 40S ribosomal protein S13 / 40S ribosomal protein S2 / Large ribosomal subunit protein uL6 / 40S ribosomal protein S12 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / 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 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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-3j7r
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2644.png

Downloads & links

-
Map

FileDownload / File: emd_2644.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian ribosome in complex with Sec61. Translating active class with mRNA and hybrid tRNAs
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.39422372 - 0.67518675
Average (Standard dev.)0.00143454 (±0.02157907)
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-0.3940.6750.001

-
Supplemental data

-
Supplemental map: 80S active half1 unfil.map

File80S_active_half1_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: 80S active half2 unfil.map

File80S_active_half2_unfil.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: 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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
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: 3.9 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