+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10073 | |||||||||
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Title | Ribosome nascent chain in complex with SecA | |||||||||
Map data | Ribosome nascent chain in complex with SecA | |||||||||
Sample |
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Keywords | Ribosome nascent chain in complex with SecA / RIBOSOME | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Jomaa A / Wang S | |||||||||
Funding support | Switzerland, United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10073.map.gz | 116 MB | EMDB map data format | |
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Header (meta data) | emd-10073-v30.xml emd-10073.xml | 53.3 KB 53.3 KB | Display Display | EMDB header |
Images | emd_10073.png | 70 KB | ||
Filedesc metadata | emd-10073.cif.gz | 11.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10073 | HTTPS FTP |
-Validation report
Summary document | emd_10073_validation.pdf.gz | 823.2 KB | Display | EMDB validaton report |
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Full document | emd_10073_full_validation.pdf.gz | 822.7 KB | Display | |
Data in XML | emd_10073_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_10073_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10073 | HTTPS FTP |
-Related structure data
Related structure data | 6s0kMC 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_10073.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ribosome nascent chain in complex with SecA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 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 : ribosome nascent chain in complex with SecA
+Supramolecule #1: ribosome nascent chain in complex with SecA
+Supramolecule #2: ribosome
+Supramolecule #3: SecA
+Supramolecule #4: nascent chain
+Macromolecule #1: tRNA-CCA
+Macromolecule #2: 23S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: 50S ribosomal protein L2
+Macromolecule #5: 50S ribosomal protein L3
+Macromolecule #6: 50S ribosomal protein L4
+Macromolecule #7: 50S ribosomal protein L5
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L9
+Macromolecule #10: 50S ribosomal protein L10
+Macromolecule #11: 50S ribosomal protein L11
+Macromolecule #12: 50S ribosomal protein L13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15
+Macromolecule #15: 50S ribosomal protein L16
+Macromolecule #16: 50S ribosomal protein L17
+Macromolecule #17: 50S ribosomal protein L18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: 50S ribosomal protein L20
+Macromolecule #20: 50S ribosomal protein L21
+Macromolecule #21: 50S ribosomal protein L22
+Macromolecule #22: 50S ribosomal protein L23
+Macromolecule #23: 50S ribosomal protein L24
+Macromolecule #24: 50S ribosomal protein L25
+Macromolecule #25: 50S ribosomal protein L27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: 50S ribosomal protein L30
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: Protein translocase subunit SecA
+Macromolecule #35: Cytoskeleton protein RodZ
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | prepared using in-vitro translation system |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: 70S ribosome |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 37334 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |