+Open data
-Basic information
Entry | Database: PDB / ID: 5gaf | ||||||
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Title | RNC in complex with SRP | ||||||
Components |
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Keywords | RIBOSOME / srp / sr | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / signal recognition particle / alkaline phosphatase activity / signal-recognition-particle GTPase / hydrogenase (acceptor) activity / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response ...oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / signal recognition particle / alkaline phosphatase activity / signal-recognition-particle GTPase / hydrogenase (acceptor) activity / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response / phosphoprotein phosphatase activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / dephosphorylation / : / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / protein dephosphorylation / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / outer membrane-bounded periplasmic space / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / periplasmic space / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / magnesium ion binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Jomaa, A. / Boehringer, D. / Leibundgut, M. / Ban, N. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon. Authors: Ahmad Jomaa / Daniel Boehringer / Marc Leibundgut / Nenad Ban / Abstract: Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here ...Co-translational protein targeting to membranes is a universally conserved process. Central steps include cargo recognition by the signal recognition particle and handover to the Sec translocon. Here we present snapshots of key co-translational-targeting complexes solved by cryo-electron microscopy at near-atomic resolution, establishing the molecular contacts between the Escherichia coli translating ribosome, the signal recognition particle and the translocon. Our results reveal the conformational changes that regulate the latching of the signal sequence, the release of the heterodimeric domains of the signal recognition particle and its receptor, and the handover of the signal sequence to the translocon. We also observe that the signal recognition particle and the translocon insert-specific structural elements into the ribosomal tunnel to remodel it, possibly to sense nascent chains. Our work provides structural evidence for a conformational state of the signal recognition particle and its receptor primed for translocon binding to the ribosome-nascent chain complex. | ||||||
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 | 5gaf.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5gaf.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5gaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/5gaf ftp://data.pdbj.org/pub/pdb/validation_reports/ga/5gaf | HTTPS FTP |
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-Related structure data
Related structure data | 8002MC 8000C 8001C 8003C 8004C 5gadC 5gaeC 5gagC 5gahC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules 12AB
#1: RNA chain | Mass: 36502.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 899721066 |
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#2: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: RNA chain | Mass: 934972.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 170787319 |
#4: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 817146391 |
+50S ribosomal protein ... , 30 types, 30 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef
-Protein / Protein/peptide , 2 types, 2 molecules ik
#35: Protein | Mass: 43545.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: *****Notes: Less defined regions were replaced with UNK residues. Full sequence is below: ...Details: *****Notes: Less defined regions were replaced with UNK residues. Full sequence is below: MFDNLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVKEKAVGHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKEAKLKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNEALPLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMGDVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMKKGGMAKMMRSMKGMMPPGFPGR Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AGD7*PLUS |
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#36: Protein/peptide | Mass: 1981.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00634*PLUS |
-Non-polymers , 3 types, 433 molecules
#37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ZN / | #39: Chemical | ChemComp-GNP / | |
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-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: Ribosome nascent chain complex with SRP / Type: RIBOSOME / Entity ID: #1-#37 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78 K / Temperature (min): 78 K |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16407 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |