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- EMDB-3045: Density map of the scanning state of the mammalian SRP-ribosome c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3045 | |||||||||
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Title | Density map of the scanning state of the mammalian SRP-ribosome complex | |||||||||
![]() | This is the final masked and sharpened reconstruction | |||||||||
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![]() | ribosomes / SRP / mammal / translocation | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 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) | ![]() ![]() | 8.4 KB 8.4 KB | Display Display | ![]() |
Images | ![]() | 354.4 KB | ||
Others | ![]() ![]() | 224.9 MB 224.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3janMC ![]() 3037C ![]() 3046C ![]() 3jajC 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 the final masked and sharpened reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 3045 half map 1.map
File | emd_3045_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3045 half map 2.map
File | emd_3045_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of the mammalian ribosome and SRP in its scanning mode
Entire | Name: Complex of the mammalian ribosome and SRP in its scanning mode |
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Components |
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-Supramolecule #1000: Complex of the mammalian ribosome and SRP in its scanning mode
Supramolecule | Name: Complex of the mammalian ribosome and SRP in its scanning mode type: sample / ID: 1000 / Oligomeric state: Heterodimer of mammalian ribosome and SRP / 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 complex / 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 pH 7.5, 200 mM 469 KAc, 15 mM MgAc2, and 1 mM DTT |
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Grid | Details: glow-discharged holey carbon grids (Quantifoil R2/2), coated with a ~70 angstrom thick layer of amorphous carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: sample was applied to the grid, followed by a 30 s incubation at 4C, 3 s of blotting |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 14, 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: 2.0 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
Details | The particles were selected using the automated particle picker in Relion |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Relion Details: Final maps were calculated from two averaged data sets Number images used: 27627 |