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Yorodumi- EMDB-1484: Ribosome Binding of a Single Copy of the SecY Complex: Implicatio... -
+Open data
-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 | |||||||||
Map data | Escherichia coli ribosome secY complex | |||||||||
Sample |
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Keywords | ribosome / secY / translocation / electron microscopy | |||||||||
Function / homology | Function and homology information intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / protein transmembrane transporter activity ...intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / protein transmembrane transporter activity / protein secretion / protein targeting / 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 / four-way junction DNA binding / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / protein transport / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.6 Å | |||||||||
Authors | 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 | |||||||||
Citation | Journal: Mol Cell / Year: 2007 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1484.map.gz | 10.7 MB | EMDB map data format | |
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Header (meta data) | emd-1484-v30.xml emd-1484.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | 1484.png | 666 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1484 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1484 | HTTPS FTP |
-Related structure data
Related structure data | 3bo0MC 3bo1MC 4v7iM 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_1484.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Escherichia coli ribosome secY complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 3.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
-Image processing
CTF correction | Details: by micrograph |
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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 |
Details | 1900 classes were used in EMAN 3D refinement |
-Atomic model buiding 1
Initial model | (PDB ID: , 2i2t 2i2p |
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Software | Name: coot |
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: |