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Yorodumi- EMDB-6485: Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6485 | |||||||||
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Title | Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps | |||||||||
Map data | Cryo EM reconstruction of SecM-Pro-RNC ( ribosomal-nascent-peptide-complex) without 50S-tRNA mask | |||||||||
Sample |
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Keywords | electron microscopy / single particle analysis / ribosome stalling | |||||||||
Function / homology | Function and homology information outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / monoatomic ion transport / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / cell outer membrane / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / outer membrane-bounded periplasmic space / 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 / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / symbiont entry into host cell / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA damage response / DNA binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Zhang J / Pan XJ / Yan KG / Sun S / Gao N / Sui SF | |||||||||
Citation | Journal: Elife / Year: 2015 Title: Mechanisms of ribosome stalling by SecM at multiple elongation steps. Authors: Jun Zhang / Xijiang Pan / Kaige Yan / Shan Sun / Ning Gao / Sen-Fang Sui / Abstract: Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA- ...Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling. However, the underlying molecular mechanism is still not clear at the atomic level. Here, we present two cryo-EM structures of the SecM-stalled ribosomes at 3.3-3.7 Å resolution, which reveal two different stalling mechanisms at distinct elongation steps of the translation cycle: one is due to the inactivation of ribosomal peptidyl-transferase center which inhibits peptide bond formation with the incoming prolyl-tRNA; the other is the prolonged residence of the peptidyl-RNA at the hybrid A/P site which inhibits the full-scale tRNA translocation. These results demonstrate an elegant control of translation cycle by regulatory peptides through a continuous, dynamic reshaping of the functional center of the ribosome. | |||||||||
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_6485.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-6485-v30.xml emd-6485.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6485_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_6485.tif | 130 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6485 | HTTPS FTP |
-Validation report
Summary document | emd_6485_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_6485_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_6485_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6485 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6485 | HTTPS FTP |
-Related 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_6485.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM reconstruction of SecM-Pro-RNC ( ribosomal-nascent-peptide-complex) without 50S-tRNA mask | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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 : SecM-Pro-RNC(ribosome-nascent-peptide-complex) complex without mask
Entire | Name: SecM-Pro-RNC(ribosome-nascent-peptide-complex) complex without mask |
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Components |
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-Supramolecule #1000: SecM-Pro-RNC(ribosome-nascent-peptide-complex) complex without mask
Supramolecule | Name: SecM-Pro-RNC(ribosome-nascent-peptide-complex) complex without mask type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 2.3 MDa |
-Supramolecule #1: SecM-Pro-RNC without mask
Supramolecule | Name: SecM-Pro-RNC without mask / type: complex / ID: 1 / Name.synonym: SecM-Pro-stalled RNC without mask / Recombinant expression: Yes / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: Escherichia coli MG1655 / Recombinant plasmid: pET21 |
Molecular weight | Theoretical: 2.3 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Details: 20mM HEPES, 50mM KOAc, 6mM Mg[OAc]2, 1mM DTT, 500 ug/ml chloramphenicol,0.05% Nikkol,0.5% pill/ml Complete EDTA-free Protease inhibitor cocktail,0.1 U/ml RNasin and 125mM sucrose |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 seconds before plunging |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Date | May 8, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 4 µm / Number real images: 3908 / Average electron dose: 16 e/Å2 Details: Every image is the average of 14 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37878 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TITAN KRIOS |
Date | Jun 16, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 4 µm / Number real images: 3908 / Average electron dose: 16 e/Å2 Details: Every image is the average of 14 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37878 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #3
Microscopy ID | 3 |
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Microscope | FEI TITAN KRIOS |
Date | Aug 30, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 4 µm / Number real images: 3908 / Average electron dose: 16 e/Å2 Details: Every image is the average of 14 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37878 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera, EMFit, Coot |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |