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- EMDB-3037: Density map of the engaged state of the mammalian SRP-ribosome complex -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3037 | |||||||||
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Title | Density map of the engaged state of the mammalian SRP-ribosome complex | |||||||||
![]() | This is a sharpened post-processed, masked map | |||||||||
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![]() | ribosomes / SRP / mammal / translocation | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
![]() | Voorhees RM / Hegde RS | |||||||||
![]() | ![]() Title: Structures of the scanning and engaged states of the mammalian SRP-ribosome complex. Authors: Rebecca M Voorhees / Ramanujan S Hegde / ![]() Abstract: The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially ...The universally conserved signal recognition particle (SRP) is essential for the biogenesis of most integral membrane proteins. SRP scans the nascent chains of translating ribosomes, preferentially engaging those with hydrophobic targeting signals, and delivers these ribosome-nascent chain complexes to the membrane. Here, we present structures of native mammalian SRP-ribosome complexes in the scanning and engaged states. These structures reveal the near-identical SRP architecture of these two states, show many of the SRP-ribosome interactions at atomic resolution, and suggest how the polypeptide-binding M domain selectively engages hydrophobic signals. The scanning M domain, pre-positioned at the ribosomal exit tunnel, is auto-inhibited by a C-terminal amphipathic helix occluding its hydrophobic binding groove. Upon engagement, the hydrophobic targeting signal displaces this amphipathic helix, which then acts as a protective lid over the signal. Biochemical experiments suggest how scanning and engagement are coordinated with translation elongation to minimize exposure of hydrophobic signals during membrane targeting. | |||||||||
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 | ![]() | 31.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.3 KB 8.3 KB | Display Display | ![]() |
Images | ![]() | 325.1 KB | ||
Others | ![]() ![]() | 224.6 MB 224.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jajMC ![]() 3045C ![]() 3046C ![]() 3janC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a sharpened post-processed, masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 3037 half map 1.map
File | emd_3037_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3037 half map 2.map
File | emd_3037_half_map_2.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 the signal recognition particl...
Entire | Name: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate |
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Components |
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-Supramolecule #1000: Mammalian ribosome in complex with the signal recognition particl...
Supramolecule | Name: Mammalian ribosome in complex with the signal recognition particle interacting with its hydrophobic substrate type: sample / ID: 1000 Oligomeric state: monomeric ribosome with monomeric signal recognition particle Number unique components: 2 |
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-Supramolecule #1: mammalian ribosome
Supramolecule | Name: mammalian ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Signal recognition particle
Macromolecule | Name: Signal recognition particle / type: rna / ID: 1 / Name.synonym: SRP / Details: Ribonucleoprotein particle / Classification: OTHER / Structure: OTHER / Synthetic?: 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: 50 mM HEPES, 200 mM KAc, 15 mM MgAc2, and 1 mM DTT |
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Grid | Details: Quantifoil R2/2 400 mesh copper grids. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: 3uL of sampled was incubated on the grid for 30 seconds before blotting for 3 second |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jun 16, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
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: 3.75 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 52061 |