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Yorodumi- EMDB-12633: Mammalian pre-termination 80S ribosome with Empty-A site bound by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12633 | |||||||||
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Title | Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / laminin receptor activity / regulation of G1 to G0 transition / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / G1 to G0 transition / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / ribosomal small subunit export from nucleus / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / spindle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / ribosome binding / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / heparin binding / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / postsynapse / perikaryon / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / cell cycle / cell division / DNA repair / mRNA binding / centrosome / apoptotic process / synapse / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Powers KT / Yadav SKN / Bufton JC / Schaffitzel C | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA. Authors: Kyle T Powers / Flint Stevenson-Jones / Sathish K N Yadav / Beate Amthor / Joshua C Bufton / Ufuk Borucu / Dakang Shen / Jonas P Becker / Daria Lavysh / Matthias W Hentze / Andreas E Kulozik ...Authors: Kyle T Powers / Flint Stevenson-Jones / Sathish K N Yadav / Beate Amthor / Joshua C Bufton / Ufuk Borucu / Dakang Shen / Jonas P Becker / Daria Lavysh / Matthias W Hentze / Andreas E Kulozik / Gabriele Neu-Yilik / Christiane Schaffitzel / Abstract: Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding ...Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3'CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1's accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production. | |||||||||
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_12633.map.gz | 15.5 MB | EMDB map data format | |
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Header (meta data) | emd-12633-v30.xml emd-12633.xml | 95.6 KB 95.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12633_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_12633.png | 121.8 KB | ||
Masks | emd_12633_msk_1.map | 103 MB | Mask map | |
Others | emd_12633_half_map_1.map.gz emd_12633_half_map_2.map.gz | 80.7 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12633 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12633 | HTTPS FTP |
-Validation report
Summary document | emd_12633_validation.pdf.gz | 828.5 KB | Display | EMDB validaton report |
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Full document | emd_12633_full_validation.pdf.gz | 828.1 KB | Display | |
Data in XML | emd_12633_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_12633_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12633 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12633 | HTTPS FTP |
-Related structure data
Related structure data | 7nwiMC 7nwgC 7nwhC 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_12633.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12633_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12633_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12633_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian pre-termination 80S ribosome with Empty-A site bound by...
+Supramolecule #1: Mammalian pre-termination 80S ribosome with Empty-A site bound by...
+Macromolecule #1: L8
+Macromolecule #2: uL3
+Macromolecule #3: 60S ribosomal protein L4
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: uL30
+Macromolecule #7: 60S ribosomal protein L7a
+Macromolecule #8: L9
+Macromolecule #9: 60S ribosomal protein L10
+Macromolecule #10: Ribosomal protein L11
+Macromolecule #11: L13
+Macromolecule #12: Ribosomal protein L14
+Macromolecule #13: Ribosomal protein L15
+Macromolecule #14: L13a
+Macromolecule #15: L17
+Macromolecule #16: Ribosomal_L18e/L15P domain-containing protein
+Macromolecule #17: 60S ribosomal protein L19
+Macromolecule #18: L18a
+Macromolecule #19: eL21
+Macromolecule #20: 60S ribosomal protein L22
+Macromolecule #21: eL14
+Macromolecule #22: 60S ribosomal protein L24-like protein
+Macromolecule #23: uL23
+Macromolecule #24: Ribosomal protein L26
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: uL15
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: 60S ribosomal protein L34
+Macromolecule #33: uL29
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: Ribosomal protein L37
+Macromolecule #36: L38
+Macromolecule #37: ribosomal protein eL39
+Macromolecule #38: 60S ribosomal protein L40
+Macromolecule #39: 60s ribosomal protein l41
+Macromolecule #40: LOW QUALITY PROTEIN: 60S ribosomal protein L36a
+Macromolecule #41: ribosomal protein eL43
+Macromolecule #42: eL28
+Macromolecule #43: 60S acidic ribosomal protein P0
+Macromolecule #44: L12
+Macromolecule #45: 40S ribosomal protein SA
+Macromolecule #46: 40S ribosomal protein S3a
+Macromolecule #47: 40S ribosomal protein S2
+Macromolecule #48: 40S ribosomal protein S3
+Macromolecule #49: S4
+Macromolecule #50: Ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S6
+Macromolecule #52: ribosomal protein eS7
+Macromolecule #53: 40S ribosomal protein S8
+Macromolecule #54: 40S ribosomal protein S9
+Macromolecule #55: S10_plectin domain-containing protein
+Macromolecule #56: 40S ribosomal protein S11
+Macromolecule #57: 40S ribosomal protein S12
+Macromolecule #58: ribosomal protein uS15
+Macromolecule #59: S14
+Macromolecule #60: 40S ribosomal protein uS19
+Macromolecule #61: Rps16 protein
+Macromolecule #62: S17
+Macromolecule #63: ribosomal protein uS13
+Macromolecule #64: S19
+Macromolecule #65: Ribosomal_S10 domain-containing protein
+Macromolecule #66: S21
+Macromolecule #67: Ribosomal protein S15a
+Macromolecule #68: Ribosomal protein S23
+Macromolecule #69: 40S ribosomal protein S24
+Macromolecule #70: 40S ribosomal protein S25
+Macromolecule #71: 40S ribosomal protein S26
+Macromolecule #72: 40S ribosomal protein S27
+Macromolecule #73: 40S ribosomal protein S28
+Macromolecule #74: ribosomal protein uS14
+Macromolecule #75: 40S ribosomal protein S30
+Macromolecule #76: S27a
+Macromolecule #77: ribosomal protein RACK1
+Macromolecule #78: Sec61Beta
+Macromolecule #79: P-Site tRNA
+Macromolecule #80: 28S ribosomal RNA+BlaS
+Macromolecule #81: 5S ribosomal RNA
+Macromolecule #82: 5.8S ribosomal RNA
+Macromolecule #83: 18S ribosomal RNA
+Macromolecule #84: mRNA
+Macromolecule #85: MAGNESIUM ION
+Macromolecule #86: ZINC ION
+Macromolecule #87: BLASTICIDIN S
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.63 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM HEPES pH 7.4 100 mM KOAc 5 mM Mg(Oac)2 1mM DTT |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 288.15 K / Instrument: LEICA EM GP Details: 30s sample incubation on grid followed by 1.1s blotting time.. |
Details | 165nM (OD260nm~10.5) |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Details | Collected in super-resolution mode (0.675A pixel size) |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3500 / Average exposure time: 8.0 sec. / Average electron dose: 41.92 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 79000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |