+Open data
-Basic information
Entry | Database: PDB / ID: 6s0k | |||||||||
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Title | Ribosome nascent chain in complex with SecA | |||||||||
Components |
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Keywords | RIBOSOME / Ribosome nascent chain in complex with SecA | |||||||||
Function / homology | Function and homology information cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting ...cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Jomaa, A. / Wang, S. / Shan, S. / Ban, N. | |||||||||
Funding support | Switzerland, United States, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA. Authors: Shuai Wang / Ahmad Jomaa / Mateusz Jaskolowski / Chien-I Yang / Nenad Ban / Shu-Ou Shan / Abstract: Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent ...Cotranslational protein targeting is a conserved process for membrane protein biogenesis. In Escherichia coli, the essential ATPase SecA was found to cotranslationally target a subset of nascent membrane proteins to the SecYEG translocase at the plasma membrane. The molecular mechanism of this pathway remains unclear. Here we use biochemical and cryoelectron microscopy analyses to show that the amino-terminal amphipathic helix of SecA and the ribosomal protein uL23 form a composite binding site for the transmembrane domain (TMD) on the nascent protein. This binding mode further enables recognition of charged residues flanking the nascent TMD and thus explains the specificity of SecA recognition. Finally, we show that membrane-embedded SecYEG promotes handover of the translating ribosome from SecA to the translocase via a concerted mechanism. Our work provides a molecular description of the SecA-mediated cotranslational targeting pathway and demonstrates an unprecedented role of the ribosome in shielding nascent TMDs. | |||||||||
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 | 6s0k.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6s0k.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 6s0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s0k_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6s0k_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6s0k_validation.xml.gz | 139.5 KB | Display | |
Data in CIF | 6s0k_validation.cif.gz | 250.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s0k ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s0k | HTTPS FTP |
-Related structure data
Related structure data | 10073MC 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 , 3 types, 3 molecules 2AB
#1: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 934972.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: 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: 1476653947 |
+50S ribosomal protein ... , 30 types, 30 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef
-Protein , 2 types, 2 molecules hk
#34: Protein | Mass: 95155.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secA, azi, div / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037YQ84 |
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#35: Protein | Mass: 5823.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rodZ, SAMEA3472055_00952 / Production host: Escherichia coli (E. coli) |
-Non-polymers , 2 types, 69 molecules
#36: Chemical | ChemComp-MG / #37: Chemical | ChemComp-ZN / | |
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-Details
Has ligand of interest | N |
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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 |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: prepared using in-vitro translation system | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 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 FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37334 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5GAG Accession code: 5GAG / Source name: PDB / Type: experimental model |