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Yorodumi- EMDB-4475: Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4475 | |||||||||
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Title | Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | tmRNA SmpB trans-translation translation / RIBOSOME | |||||||||
Function / homology | Function and homology information trans-translation / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity ...trans-translation / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / large ribosomal subunit / 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 / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Escherichia coli (E. coli) / Thermus thermophilus HB27 (bacteria) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) | |||||||||
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_4475.map.gz | 18.3 MB | EMDB map data format | |
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Header (meta data) | emd-4475-v30.xml emd-4475.xml | 83.6 KB 83.6 KB | Display Display | EMDB header |
Images | emd_4475.png | 61.1 KB | ||
Filedesc metadata | emd-4475.cif.gz | 14.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4475 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4475 | HTTPS FTP |
-Validation report
Summary document | emd_4475_validation.pdf.gz | 239.5 KB | Display | EMDB validaton report |
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Full document | emd_4475_full_validation.pdf.gz | 238.6 KB | Display | |
Data in XML | emd_4475_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4475 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4475 | HTTPS FTP |
-Related structure data
Related structure data | 6q95MC 4476C 4477C 4478C 6q97C 6q98C 6q9aC C: citing same article (ref.) M: atomic model generated by this map |
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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_4475.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34 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 : 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #1: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #2: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #3: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #4: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #5: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #6: 70S ribosome bound by tmRNA-SmpB in the A site
+Supramolecule #7: 70S ribosome bound by tmRNA-SmpB in the A site
+Macromolecule #1: 16S RIBOSOMAL RNA
+Macromolecule #22: tRNA-fMet
+Macromolecule #23: tRNA-Phe
+Macromolecule #24: mRNA
+Macromolecule #34: 23S RIBOSOMAL RNA
+Macromolecule #35: 5S RIBOSOMAL RNA
+Macromolecule #60: transfer-messenger RNA (tmRNA)
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14 type Z
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein Thx
+Macromolecule #25: 50S ribosomal protein L27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: 50S ribosomal protein L30
+Macromolecule #29: 50S ribosomal protein L31
+Macromolecule #30: 50S ribosomal protein L32
+Macromolecule #31: 50S ribosomal protein L33
+Macromolecule #32: 50S ribosomal protein L34
+Macromolecule #33: 50S ribosomal protein L35
+Macromolecule #36: 50S ribosomal protein L1
+Macromolecule #37: 50S ribosomal protein L2
+Macromolecule #38: 50S ribosomal protein L3
+Macromolecule #39: 50S ribosomal protein L4
+Macromolecule #40: 50S ribosomal protein L5
+Macromolecule #41: 50S ribosomal protein L6
+Macromolecule #42: 50S ribosomal protein L9
+Macromolecule #43: 50S ribosomal protein L13
+Macromolecule #44: 50S ribosomal protein L14
+Macromolecule #45: 50S ribosomal protein L15
+Macromolecule #46: 50S ribosomal protein L16
+Macromolecule #47: 50S ribosomal protein L17
+Macromolecule #48: 50S ribosomal protein L18
+Macromolecule #49: 50S ribosomal protein L19
+Macromolecule #50: 50S ribosomal protein L20
+Macromolecule #51: 50S ribosomal protein L21
+Macromolecule #52: 50S ribosomal protein L22
+Macromolecule #53: 50S ribosomal protein L23
+Macromolecule #54: 50S ribosomal protein L24
+Macromolecule #55: 50S ribosomal protein L25
+Macromolecule #56: SsrA-binding protein
+Macromolecule #57: Nascent peptide MET-ALA
+Macromolecule #58: 50S ribosomal protein L36
+Macromolecule #59: 50S RIBOSOMAL PROTEIN L10 AND L11
+Macromolecule #61: MAGNESIUM ION
+Macromolecule #62: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: 42.0 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 |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24400 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |