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Yorodumi- EMDB-71745: Composite map of hypomethylated 80S ribosome treated with hygromycin B -
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Open data
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Basic information
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| Title | Composite map of hypomethylated 80S ribosome treated with hygromycin B | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 2'-O-methylation / ribosome / rRNA modification | |||||||||
| Function / homology | Function and homology informationmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / cytosolic large ribosomal subunit assembly / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of translational frameshifting / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / regulation of translational fidelity / translational termination / protein-RNA complex assembly / maturation of LSU-rRNA / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / cellular response to amino acid starvation / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 1.75 Å | |||||||||
Authors | Zhao Y / Li H | |||||||||
| Funding support | United States, 2 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_71745.map.gz | 766.3 MB | EMDB map data format | |
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| Header (meta data) | emd-71745-v30.xml emd-71745.xml | 101.3 KB 101.3 KB | Display Display | EMDB header |
| Images | emd_71745.png | 35.8 KB | ||
| Filedesc metadata | emd-71745.cif.gz | 19.7 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-71745 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71745 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9pn5MC ![]() 71722 ![]() 71723 ![]() 71724 ![]() 71725 M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_71745.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Hypomethylated 80S treated with hygromycin B
+Supramolecule #1: Hypomethylated 80S treated with hygromycin B
+Macromolecule #1: Small ribosomal subunit protein uS2A
+Macromolecule #2: Small ribosomal subunit protein eS1A
+Macromolecule #3: Small ribosomal subunit protein uS5
+Macromolecule #4: Small ribosomal subunit protein eS4A
+Macromolecule #5: Small ribosomal subunit protein eS6A
+Macromolecule #6: Small ribosomal subunit protein eS7A
+Macromolecule #7: Small ribosomal subunit protein eS8A
+Macromolecule #8: Small ribosomal subunit protein uS4A
+Macromolecule #9: Small ribosomal subunit protein uS17A
+Macromolecule #10: Small ribosomal subunit protein uS15
+Macromolecule #11: Small ribosomal subunit protein uS11A
+Macromolecule #12: Small ribosomal subunit protein eS21A
+Macromolecule #13: Small ribosomal subunit protein uS8A
+Macromolecule #14: Small ribosomal subunit protein uS12A
+Macromolecule #15: Small ribosomal subunit protein eS24A
+Macromolecule #16: Small ribosomal subunit protein eS26B
+Macromolecule #17: Small ribosomal subunit protein eS27A
+Macromolecule #18: Small ribosomal subunit protein eS30A
+Macromolecule #19: Small ribosomal subunit protein uS3
+Macromolecule #20: Small ribosomal subunit protein uS7
+Macromolecule #21: Small ribosomal subunit protein eS10A
+Macromolecule #22: Small ribosomal subunit protein uS19
+Macromolecule #23: Small ribosomal subunit protein uS9A
+Macromolecule #24: Small ribosomal subunit protein eS17A
+Macromolecule #25: Small ribosomal subunit protein uS13A
+Macromolecule #26: Small ribosomal subunit protein eS19A
+Macromolecule #27: Small ribosomal subunit protein uS10
+Macromolecule #28: Small ribosomal subunit protein eS25A
+Macromolecule #29: Small ribosomal subunit protein eS28A
+Macromolecule #30: Small ribosomal subunit protein uS14A
+Macromolecule #31: Small ribosomal subunit protein RACK1
+Macromolecule #32: Ubiquitin-ribosomal protein eS31 fusion protein
+Macromolecule #33: Small ribosomal subunit protein eS12
+Macromolecule #35: 60S ribosomal protein L2-A
+Macromolecule #36: Large ribosomal subunit protein uL3
+Macromolecule #37: 60S ribosomal protein L4-A
+Macromolecule #41: 60S ribosomal protein L5
+Macromolecule #42: Large ribosomal subunit protein eL6A
+Macromolecule #43: 60S ribosomal protein L7-A
+Macromolecule #44: Large ribosomal subunit protein eL8A
+Macromolecule #45: Large ribosomal subunit protein uL6A
+Macromolecule #46: Large ribosomal subunit protein uL16
+Macromolecule #47: 60S ribosomal protein L11-A
+Macromolecule #48: 60S ribosomal protein L13-A
+Macromolecule #49: 60S ribosomal protein L14-A
+Macromolecule #50: Large ribosomal subunit protein eL15A
+Macromolecule #51: Large ribosomal subunit protein uL13A
+Macromolecule #52: 60S ribosomal protein L17-A
+Macromolecule #53: 60S ribosomal protein L18-A
+Macromolecule #54: 60S ribosomal protein L19-A
+Macromolecule #55: Large ribosomal subunit protein eL20A
+Macromolecule #56: 60S ribosomal protein L21-A
+Macromolecule #57: 60S ribosomal protein L22-A
+Macromolecule #58: 60S ribosomal protein L23-A
+Macromolecule #59: Large ribosomal subunit protein eL24A
+Macromolecule #60: 60S ribosomal protein L25
+Macromolecule #61: 60S ribosomal protein L26-A
+Macromolecule #62: 60S ribosomal protein L27-A
+Macromolecule #63: 60S ribosomal protein L28
+Macromolecule #64: Large ribosomal subunit protein eL29
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: 60S ribosomal protein L31-A
+Macromolecule #67: 60S ribosomal protein L32
+Macromolecule #68: 60S ribosomal protein L33-A
+Macromolecule #69: 60S ribosomal protein L34-A
+Macromolecule #70: 60S ribosomal protein L35-A
+Macromolecule #71: 60S ribosomal protein L36-A
+Macromolecule #72: 60S ribosomal protein L37-A
+Macromolecule #73: 60S ribosomal protein L38
+Macromolecule #74: 60S ribosomal protein L39
+Macromolecule #75: Ubiquitin-ribosomal protein eL40A fusion protein
+Macromolecule #76: Small ribosomal subunit protein eS32A
+Macromolecule #77: Large ribosomal subunit protein eL42A
+Macromolecule #78: 60S ribosomal protein L43-A
+Macromolecule #34: 18S rRNA
+Macromolecule #38: 25S rRNA
+Macromolecule #39: 5S rRNA
+Macromolecule #40: 5.8S rRNA
+Macromolecule #79: MAGNESIUM ION
+Macromolecule #80: POTASSIUM ION
+Macromolecule #81: ZINC ION
+Macromolecule #82: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States, 2 items
Citation












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Processing
FIELD EMISSION GUN
