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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2650 | |||||||||
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Title | Structure of the mammalian ribosome-Sec61 complex | |||||||||
![]() | Final map for mammalian ribosome in complex with Sec61 in idle configuration with the large subunit masked along refinement | |||||||||
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![]() | translation / ribosome / mammalian / sec61 | |||||||||
Function / homology | ![]() : / 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 / embryonic brain development / translation at presynapse / cytoplasmic side of rough endoplasmic reticulum membrane / 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 / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of signal transduction by p53 class mediator / organelle membrane / ubiquitin ligase inhibitor activity / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-RNA complex assembly / protein targeting / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / rRNA processing / large ribosomal subunit / protein tag activity / protein transport / ribosome biogenesis / presynapse / regulation of translation / heparin binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / membrane => GO:0016020 / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / glutamatergic synapse / synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Voorhees RM / Fernandez IS / Scheres SHW / Hegde R | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.6 KB 8.6 KB | Display Display | ![]() |
Images | ![]() | 307.4 KB | ||
Others | ![]() ![]() | 282.6 MB 282.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 337.1 KB | Display | ![]() |
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Full document | ![]() | 336.7 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j7qMC ![]() 2644C ![]() 2646C ![]() 2649C ![]() 3j7oC ![]() 3j7pC ![]() 3j7rC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Final map for mammalian ribosome in complex with Sec61 in idle configuration with the large subunit masked along refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 60S idle half1 unfil.map
File | 60S_idle_half1_unfil.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: 60S idle half2 unfil.map
File | 60S_idle_half2_unfil.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mammalian ribosome in complex with Sec61 in a idle configuration ...
Entire | Name: Mammalian ribosome in complex with Sec61 in a idle configuration 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 in a idle configuration ...
Supramolecule | Name: 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 |
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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: ![]() ![]() |
-Macromolecule #1: Sec61
Macromolecule | Name: Sec61 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 80019 |