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Yorodumi- PDB-4ue4: Structural basis for targeting and elongation arrest of Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ue4 | ||||||
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Title | Structural basis for targeting and elongation arrest of Bacillus signal recognition particle | ||||||
Components |
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Keywords | TRANSLATION / SIGNAL RECOGNITION PARTICLE (SRP) / STALLED-RIBOSOME / TRANSLOCATION / MIFM STALLING | ||||||
Function / homology | Function and homology information FtsQBL complex / divisome complex / signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / FtsZ-dependent cytokinesis / division septum assembly / SRP-dependent cotranslational protein targeting to membrane, translocation / cell division site ...FtsQBL complex / divisome complex / signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / FtsZ-dependent cytokinesis / division septum assembly / SRP-dependent cotranslational protein targeting to membrane, translocation / cell division site / cell division / GTPase activity / GTP binding / ATP hydrolysis activity / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4ue4.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ue4.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ue4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ue4_validation.pdf.gz | 825.3 KB | Display | wwPDB validaton report |
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Full document | 4ue4_full_validation.pdf.gz | 946.8 KB | Display | |
Data in XML | 4ue4_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 4ue4_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/4ue4 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/4ue4 | HTTPS FTP |
-Related structure data
Related structure data | 2843MC 2844C 4ue5C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: RNA chain | Mass: 85909.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) References: GenBank: 40130 |
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#2: Protein/peptide | Mass: 2466.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) References: UniProt: P06136*PLUS |
#3: Protein | Mass: 11660.719 Da / Num. of mol.: 1 / Fragment: M DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37105 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: BACILLUS SUBTILIS MIFM STALLED RIBOSOME IN COMPLEX WITH SIGNAL RECOGNITION PARTICLE (SRP) Type: RIBOSOME |
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Buffer solution | Name: HEPERS 20 MM, KOAC 150 MM, MG(OAC)2 10MM, NIKKOL 0.005%, DTT 1MM, 2% GLYCEROL pH: 7.6 Details: HEPERS 20 MM, KOAC 150 MM, MG(OAC)2 10MM, NIKKOL 0.005%, DTT 1MM, 2% GLYCEROL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Dec 10, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) |
-Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: MICROGRAPH | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 7 Å / Num. of particles: 75900 / Actual pixel size: 0.953 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2843. (DEPOSITION ID: 12993). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Details: METHOD--RIGID BODY | ||||||||||||
Refinement | Highest resolution: 7 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7 Å
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