+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2646 | |||||||||
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Title | Structure of the mammalian ribosome-Sec61 complex | |||||||||
Map data | Mammalian ribosome in complex with Sec61. Class with eEF2 | |||||||||
Sample |
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Keywords | translation / 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 | |||||||||
Biological species | Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Voorhees RM / Fernandez IS / Scheres SHW / Hegde R | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2646.map.gz | 31.8 MB | EMDB map data format | |
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Header (meta data) | emd-2646-v30.xml emd-2646.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | EMD-2646.png | 330.4 KB | ||
Others | emd_2646_half_map_1.map emd_2646_half_map_2.map | 282.6 MB 282.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2646 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2646 | HTTPS FTP |
-Validation report
Summary document | emd_2646_validation.pdf.gz | 340.9 KB | Display | EMDB validaton report |
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Full document | emd_2646_full_validation.pdf.gz | 340.5 KB | Display | |
Data in XML | emd_2646_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2646 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2646 | HTTPS FTP |
-Related structure data
Related structure data | 3j7pMC 2644C 2649C 2650C 3j7oC 3j7qC 3j7rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2646.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mammalian ribosome in complex with Sec61. Class with eEF2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 2646 half map 1.map
File | emd_2646_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 2646 half map 2.map
File | emd_2646_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mammalian ribosome in complex with Sec61 with the large subunit (...
Entire | Name: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing. |
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Components |
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-Supramolecule #1000: Mammalian ribosome in complex with Sec61 with the large subunit (...
Supramolecule | Name: Mammalian ribosome in complex with Sec61 with the large subunit (60S) masked during processing. type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Mammalian ribosome
Supramolecule | Name: Mammalian ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / synonym: Pig / Tissue: pancreas |
-Macromolecule #1: Sec61
Macromolecule | Name: Sec61 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50mM hepes, 200mM K-acetate, 15mM Mg-acetate, 1mM DTT |
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Grid | Details: Quantifoil R2/2 400 mesh copper grids. |
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Date | Apr 7, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1900 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80019 |