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Yorodumi- EMDB-2844: Structural basis for targeting and elongation arrest of Bacillus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2844 | |||||||||
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Title | Structural basis for targeting and elongation arrest of Bacillus signal recognition particle | |||||||||
Map data | mammalian signal recognition particle bound to ribosome nascent chain complex. | |||||||||
Sample |
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Keywords | Signal recognition particle (SRP) / Stalled Ribosome | |||||||||
Function / homology | Function and homology information SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / absorption of visible light / signal recognition particle binding / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / 11-cis retinal binding ...SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / endoplasmic reticulum signal peptide binding / granulocyte differentiation / absorption of visible light / signal recognition particle binding / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / signal-recognition-particle GTPase / negative regulation of translational elongation / protein targeting to ER / 7S RNA binding / : / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / plasma membrane => GO:0005886 / phototransduction / photoreceptor outer segment / visual perception / neutrophil chemotaxis / photoreceptor disc membrane / GDP binding / membrane => GO:0016020 / nuclear speck / G protein-coupled receptor signaling pathway / GTPase activity / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Triticum (plant) / Canis lupus familiaris (dog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Beckert B / Kedrov A / Sohmen D / Kempf G / Wild K / Sinning I / Stahlberg H / Wilson D N / Beckmann R | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Authors: Bertrand Beckert / Alexej Kedrov / Daniel Sohmen / Georg Kempf / Klemens Wild / Irmgard Sinning / Henning Stahlberg / Daniel N Wilson / Roland Beckmann / Abstract: The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ...The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ribosomes are slowed down by the Alu domain of SRP to allow efficient targeting. In prokaryotes, however, little is known about the structure and function of Alu domain-containing SRPs. Here, we report a complete molecular model of SRP from the Gram-positive bacterium Bacillus subtilis, based on cryo-EM. The SRP comprises two subunits, 6S RNA and SRP54 or Ffh, and it facilitates elongation slowdown similarly to its eukaryotic counterpart. However, protein contacts with the small ribosomal subunit observed for the mammalian Alu domain are substituted in bacteria by RNA-RNA interactions of 6S RNA with the α-sarcin-ricin loop and helices H43 and H44 of 23S rRNA. Our findings provide a structural basis for cotranslational targeting and RNA-driven elongation arrest in prokaryotes. | |||||||||
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_2844.map.gz | 260.7 MB | EMDB map data format | |
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Header (meta data) | emd-2844-v30.xml emd-2844.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_2844.tif | 3.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2844 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2844 | HTTPS FTP |
-Validation report
Summary document | emd_2844_validation.pdf.gz | 281.3 KB | Display | EMDB validaton report |
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Full document | emd_2844_full_validation.pdf.gz | 280.3 KB | Display | |
Data in XML | emd_2844_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2844 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2844 | HTTPS FTP |
-Related structure data
Related structure data | 4ue5MC 2843C 4ue4C 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_2844.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | mammalian signal recognition particle bound to ribosome nascent chain complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : mammalian signal recognition particle bound to ribosome nascent c...
Entire | Name: mammalian signal recognition particle bound to ribosome nascent chain complex |
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Components |
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-Supramolecule #1000: mammalian signal recognition particle bound to ribosome nascent c...
Supramolecule | Name: mammalian signal recognition particle bound to ribosome nascent chain complex type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: SRP-bound 80S ribosome
Supramolecule | Name: SRP-bound 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Triticum (plant) |
Molecular weight | Experimental: 3 MDa / Theoretical: 3 MDa |
-Macromolecule #1: signal recognition particle
Macromolecule | Name: signal recognition particle / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Canis lupus familiaris (dog) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Mar 3, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 3627 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Automated particle selection was performed using the program Signature.Three dimensional reconstructions were then performed using the SPIDER software package. |
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CTF correction | Details: micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 19096 |