+Open data
-Basic information
Entry | Database: PDB / ID: 3j7r | |||||||||||||||
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Title | Structure of the translating mammalian ribosome-Sec61 complex | |||||||||||||||
Components |
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Keywords | RIBOSOME / mammalian / Sec61 / translocation / translation | |||||||||||||||
Function / homology | Function and homology information Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / : ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / 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) / pronephric nephron development / Sec61 translocon complex / protein-transporting ATPase activity / protein insertion into ER membrane / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane, translocation / translation at presynapse / embryonic brain development / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / carboxylic acid metabolic process / signal sequence binding / post-translational protein targeting to membrane, translocation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / RHO GTPases Activate Formins / neural crest cell differentiation / negative regulation of phagocytosis / regulation of establishment of cell polarity / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / 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 mitochondrial depolarization / negative regulation of Wnt signaling pathway / negative regulation of peptidyl-serine phosphorylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / protein transmembrane transporter activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein targeting / protein-RNA complex assembly / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of intrinsic apoptotic signaling pathway / translation regulator activity / signaling adaptor activity / negative regulation of smoothened 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) / tricarboxylic acid cycle / gastrulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / SH2 domain binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cyclin binding / rescue of stalled ribosome / ribosomal large subunit biogenesis / positive regulation of GTPase activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / innate immune response in mucosa / positive regulation of translation / neural tube closure / small-subunit processome / mRNA 3'-UTR binding / cellular response to glucose stimulus / protein kinase C binding Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
Authors | Voorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S. | |||||||||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j7r.cif.gz | 5.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j7r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3j7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j7r_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3j7r_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3j7r_validation.xml.gz | 385.5 KB | Display | |
Data in CIF | 3j7r_validation.cif.gz | 652.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/3j7r ftp://data.pdbj.org/pub/pdb/validation_reports/j7/3j7r | HTTPS FTP |
-Related structure data
Related structure data | 2644MC 2646C 2649C 2650C 3j7oC 3j7pC 3j7qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 7 types, 7 molecules 578S2S4S5S6
#1: RNA chain | Mass: 1206101.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
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#2: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 371913672 |
#3: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 115552481 |
#50: RNA chain | Mass: 561958.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 37956930 |
#84: RNA chain | Mass: 3039.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
#85: RNA chain | Mass: 23874.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
#86: RNA chain | Mass: 24484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
+Ribosomal protein ... , 76 types, 76 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein , 2 types, 2 molecules 12
#47: Protein | Mass: 43496.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A4X1TV07 |
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#48: Protein | Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480WFL1 |
-Protein/peptide , 1 types, 1 molecules 3
#49: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
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-Non-polymers , 2 types, 170 molecules
#87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The 80S-Sec61 complex purified from porcine pancreas / Type: RIBOSOME |
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Buffer solution | Name: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin pH: 7.5 Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil R2/2 400 mesh copper grids |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K Details: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 7, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Details: Back-thinned |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each particle | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Method: Single particle / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14723 / Nominal pixel size: 1.34 Å / Symmetry type: POINT | |||||||||||||||
Atomic model building | B value: 37 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor and FSC / Details: METHOD--Maximum likelihood | |||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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