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Yorodumi- EMDB-4478: Structure of tmRNA SmpB bound past E site of E. coli 70S ribosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4478 | |||||||||
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Title | Structure of tmRNA SmpB bound past E site of E. coli 70S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | tmRNA SmpB trans-translation translation / RIBOSOME | |||||||||
Function / homology | Function and homology information trans-translation / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...trans-translation / negative regulation of cytoplasmic translational initiation / stringent response / 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 / four-way junction DNA binding / translational termination / 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 / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / 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 / cytoplasmic translation / tRNA binding / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Rae CD | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Science / Year: 2019 Title: How a circularized tmRNA moves through the ribosome. Authors: Christopher D Rae / Yuliya Gordiyenko / V Ramakrishnan / Abstract: During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo- ...During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA. | |||||||||
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_4478.map.gz | 15.3 MB | EMDB map data format | |
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Header (meta data) | emd-4478-v30.xml emd-4478.xml | 78.3 KB 78.3 KB | Display Display | EMDB header |
Images | emd_4478.png | 72.2 KB | ||
Filedesc metadata | emd-4478.cif.gz | 14.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4478 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4478 | HTTPS FTP |
-Validation report
Summary document | emd_4478_validation.pdf.gz | 452.3 KB | Display | EMDB validaton report |
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Full document | emd_4478_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | emd_4478_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_4478_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4478 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4478 | HTTPS FTP |
-Related structure data
Related structure data | 6q9aMC 4475C 4476C 4477C 6q95C 6q97C 6q98C 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_4478.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.15 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 : Structure of tmRNA SmpB bound in state past E site of E. coli 70S...
+Supramolecule #1: Structure of tmRNA SmpB bound in state past E site of E. coli 70S...
+Supramolecule #2: ribosome
+Supramolecule #3: nascent peptide
+Supramolecule #4: SsrA-binding protein
+Supramolecule #5: tmRNA
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 16S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #5: P-site tRNA
+Macromolecule #58: tmRNA
+Macromolecule #4: Nascent peptide
+Macromolecule #6: 50S ribosomal protein L2
+Macromolecule #7: 50S ribosomal protein L3
+Macromolecule #8: 50S ribosomal protein L4
+Macromolecule #9: 50S ribosomal protein L5
+Macromolecule #10: 50S ribosomal protein L6
+Macromolecule #11: 50S ribosomal protein L9
+Macromolecule #12: 50S ribosomal protein L10
+Macromolecule #13: 50S ribosomal protein L11
+Macromolecule #14: 50S ribosomal protein L13
+Macromolecule #15: 50S ribosomal protein L14
+Macromolecule #16: 50S ribosomal protein L15
+Macromolecule #17: 50S ribosomal protein L16
+Macromolecule #18: 50S ribosomal protein L17
+Macromolecule #19: 50S ribosomal protein L18
+Macromolecule #20: 50S ribosomal protein L19
+Macromolecule #21: 50S ribosomal protein L20
+Macromolecule #22: 50S ribosomal protein L21
+Macromolecule #23: 50S ribosomal protein L22
+Macromolecule #24: 50S ribosomal protein L23
+Macromolecule #25: 50S ribosomal protein L24
+Macromolecule #26: 50S ribosomal protein L25
+Macromolecule #27: 50S ribosomal protein L27
+Macromolecule #28: 50S ribosomal protein L28
+Macromolecule #29: 50S ribosomal protein L29
+Macromolecule #30: 50S ribosomal protein L30
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #32: 50S ribosomal protein L32
+Macromolecule #33: 50S ribosomal protein L33
+Macromolecule #34: 50S ribosomal protein L34
+Macromolecule #35: 50S ribosomal protein L35
+Macromolecule #36: 50S ribosomal protein L36
+Macromolecule #37: 30S ribosomal protein S2
+Macromolecule #38: 30S ribosomal protein S3
+Macromolecule #39: 30S ribosomal protein S4
+Macromolecule #40: 30S ribosomal protein S5
+Macromolecule #41: 30S ribosomal protein S6
+Macromolecule #42: 30S ribosomal protein S7
+Macromolecule #43: 30S ribosomal protein S8
+Macromolecule #44: 30S ribosomal protein S9
+Macromolecule #45: 30S ribosomal protein S10
+Macromolecule #46: 30S ribosomal protein S11
+Macromolecule #47: 30S ribosomal protein S12
+Macromolecule #48: 30S ribosomal protein S13
+Macromolecule #49: 30S ribosomal protein S14
+Macromolecule #50: 30S ribosomal protein S15
+Macromolecule #51: 30S ribosomal protein S16
+Macromolecule #52: 30S ribosomal protein S17
+Macromolecule #53: 30S ribosomal protein S18
+Macromolecule #54: 30S ribosomal protein S19
+Macromolecule #55: 30S ribosomal protein S20
+Macromolecule #56: 30S ribosomal protein S21
+Macromolecule #57: SsrA-binding protein
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: ZINC ION
+Macromolecule #61: water
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 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: Tecnai Polara / Image courtesy: FEI Company |