+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4477 | |||||||||
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Title | Structure of tmRNA SmpB bound in P site of E. coli 70S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information trans-translation / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...trans-translation / negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / 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 / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity / translational initiation / 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 / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / : / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / ribosome biogenesis / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / molecular adaptor activity / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Rae CD | |||||||||
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_4477.map.gz | 15.8 MB | EMDB map data format | |
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Header (meta data) | emd-4477-v30.xml emd-4477.xml | 71.9 KB 71.9 KB | Display Display | EMDB header |
Images | emd_4477.png | 65.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4477 | HTTPS FTP |
-Related structure data
Related structure data | 6q98MC 4475C 4476C 4478C 6q95C 6q97C 6q9aC 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_4477.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 : tmRNA SmpB bound in A site of E. coli 70S ribosome
+Supramolecule #1: tmRNA SmpB bound in A site of E. coli 70S ribosome
+Supramolecule #2: 70S ribosome
+Supramolecule #3: tmRNA SmpB, nascent chain
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 16S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #57: transfer-messenger RNA (tmRNA)
+Macromolecule #4: SsrA-binding protein
+Macromolecule #5: 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 #58: MAGNESIUM ION
+Macromolecule #59: ZINC ION
+Macromolecule #60: 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 18018 |