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- EMDB-1484: Ribosome Binding of a Single Copy of the SecY Complex: Implicatio... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1484 | |||||||||
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Title | Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation | |||||||||
![]() | Escherichia coli ribosome secY complex | |||||||||
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![]() | ribosome / secY / translocation / electron microscopy | |||||||||
Function / homology | ![]() intracellular protein transmembrane transport / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding ...intracellular protein transmembrane transport / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / protein secretion / protein transmembrane transporter activity / 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 / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / protein transport / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / molecular adaptor activity / 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 / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.6 Å | |||||||||
![]() | Menetret JF / Schaletzky J / Clemons WM Jr / Osborne AR / Skanland SS / Denison C / Gygi SP / Kirkpatrick DS / Park E / Ludtke SJ ...Menetret JF / Schaletzky J / Clemons WM Jr / Osborne AR / Skanland SS / Denison C / Gygi SP / Kirkpatrick DS / Park E / Ludtke SJ / Rapoport TA / Akey CW | |||||||||
![]() | ![]() Title: Ribosome binding of a single copy of the SecY complex: implications for protein translocation. Authors: Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J ...Authors: Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J Ludtke / Tom A Rapoport / Christopher W Akey / ![]() Abstract: The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to ...The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 666 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 325.1 KB | Display | ![]() |
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Full document | ![]() | 324.6 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bo0MC ![]() 3bo1MC ![]() 4v7iM M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Escherichia coli ribosome secY complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.73 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Ribosome SecY complex
Entire | Name: Ribosome SecY complex |
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Components |
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-Supramolecule #1000: Ribosome SecY complex
Supramolecule | Name: Ribosome SecY complex / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 3.2 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Name.synonym: ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 3.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 Details: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM |
Grid | Details: 400 mesh Cu grids with continuous carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made / Method: 1 second blot |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Average: 90 K |
Details | About 30 percent of the data were collected at 30 degree tilt and micrographs were processed in small strips parallel to the tilt axis to correct for the defocus ramp. |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.5 µm / Number real images: 351 / Average electron dose: 20 e/Å2 / Details: Creoscitex Eversmart scanner was used / Od range: 1 / Bits/pixel: 16 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 51000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 30 |
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Image processing
Details | 1900 classes were used in EMAN 3D refinement |
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CTF correction | Details: by micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 39000 |
-Atomic model buiding 1
Initial model | (PDB ID: , ![]() 2i2t ![]() 2i2p |
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Software | Name: ![]() |
Details | Protocol: manual in O and Chimera. Loop geometry was regularized in Coot. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-3bo0: ![]() PDB-3bo1: ![]() PDB-4v7i: |