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Yorodumi- EMDB-2843: Structural basis for targeting and elongation arrest of Bacillus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2843 | |||||||||
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Title | Structural basis for targeting and elongation arrest of Bacillus signal recognition particle | |||||||||
Map data | Croy-EM reconstruction of Bacillus signal recognition particle in complex with stalled ribosome | |||||||||
Sample |
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Keywords | Signal recognition particle (SRP) / stalled-ribosome / translation / translocation / mifm stalling | |||||||||
Function / homology | Function and homology information FtsQBL complex / divisome complex / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division ...FtsQBL complex / divisome complex / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division / GTPase activity / GTP binding / ATP hydrolysis activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 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_2843.map.gz | 42.2 MB | EMDB map data format | |
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Header (meta data) | emd-2843-v30.xml emd-2843.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | EMD-2843.jpg emd_2843.jpg | 124.3 KB 124.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2843 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2843 | HTTPS FTP |
-Validation report
Summary document | emd_2843_validation.pdf.gz | 294.9 KB | Display | EMDB validaton report |
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Full document | emd_2843_full_validation.pdf.gz | 294 KB | Display | |
Data in XML | emd_2843_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2843 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2843 | HTTPS FTP |
-Related structure data
Related structure data | 4ue4MC 2844C 4ue5C 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_2843.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Croy-EM reconstruction of Bacillus signal recognition particle in complex with stalled ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.953 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 : Bacillus subtilis mifm stalled ribosome in complex with signal re...
Entire | Name: Bacillus subtilis mifm stalled ribosome in complex with signal recognition particle (SRP) |
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Components |
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-Supramolecule #1000: Bacillus subtilis mifm stalled ribosome in complex with signal re...
Supramolecule | Name: Bacillus subtilis mifm stalled ribosome in complex with signal recognition particle (SRP) type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 2 |
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Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa / Method: Sedimentation |
-Supramolecule #1: Stalled ribosome
Supramolecule | Name: Stalled ribosome / type: complex / ID: 1 Name.synonym: Signal recognition particle bound to stalled ribosome Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Macromolecule #1: Signal recognition particle
Macromolecule | Name: Signal recognition particle / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Details: Hepes 20 mM, KOAc 150 mM, Mg(OAc)2 10mM, Nikkol 0.005%, DTT 1mM, 2% glycerol |
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Grid | Details: glow discharge and support carbon |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Dec 10, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 20910 / 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: 7.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 75900 |