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Yorodumi- EMDB-10224: Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 dele... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10224 | |||||||||
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Title | Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain | |||||||||
Map data | 30S head body postprocess | |||||||||
Sample |
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Keywords | T. kodakarensis / ac4C deletion / Ribosome / cryo-EM | |||||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cytosolic ribosome assembly / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cytosolic ribosome assembly / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Matzov D / Sas-Chen A | |||||||||
Citation | Journal: Nature / Year: 2020 Title: Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / ...Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / Yuko Nobe / Chloe A Briney / Michaella J Levy / Ryan T Fuchs / G Brett Robb / Jesse Hartmann / Sunny Sharma / Qishan Lin / Laurence Florens / Michael P Washburn / Toshiaki Isobe / Thomas J Santangelo / Moran Shalev-Benami / Jordan L Meier / Schraga Schwartz / Abstract: N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics ...N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report acC-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of acC at single-nucleotide resolution. In human and yeast mRNAs, acC sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of acC across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. AcC is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of acC and its potential thermoadaptive role. Our studies quantitatively define the acC landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease. | |||||||||
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_10224.map.gz | 47.4 MB | EMDB map data format | |
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Header (meta data) | emd-10224-v30.xml emd-10224.xml | 91.5 KB 91.5 KB | Display Display | EMDB header |
Images | emd_10224.png | 84.7 KB | ||
Filedesc metadata | emd-10224.cif.gz | 16 KB | ||
Others | emd_10224_additional_1.map.gz emd_10224_additional_2.map.gz emd_10224_additional_3.map.gz emd_10224_additional_4.map.gz emd_10224_additional_5.map.gz emd_10224_additional_6.map.gz | 307.1 MB 267.2 MB 251.5 MB 22.2 MB 30.1 MB 48.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10224 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10224 | HTTPS FTP |
-Validation report
Summary document | emd_10224_validation.pdf.gz | 477.9 KB | Display | EMDB validaton report |
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Full document | emd_10224_full_validation.pdf.gz | 477.5 KB | Display | |
Data in XML | emd_10224_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_10224_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10224 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10224 | HTTPS FTP |
-Related structure data
Related structure data | 6skgMC 6skfC 6th6C 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_10224.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 30S head body postprocess | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 50S masked unsharpened
File | emd_10224_additional_1.map | ||||||||||||
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Annotation | 50S masked unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 30S body masked unsharpened
File | emd_10224_additional_2.map | ||||||||||||
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Annotation | 30S body masked unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 30S head masked unsharpened
File | emd_10224_additional_3.map | ||||||||||||
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Annotation | 30S head masked unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 30S head masked postprocess
File | emd_10224_additional_4.map | ||||||||||||
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Annotation | 30S head masked postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 50S masked postprocess
File | emd_10224_additional_5.map | ||||||||||||
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Annotation | 50S masked postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 50S masked postprocess
File | emd_10224_additional_6.map | ||||||||||||
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Annotation | 50S masked postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 70S ribosome from Thermococcus kodakarensis
+Supramolecule #1: 70S ribosome from Thermococcus kodakarensis
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #27: 23S ribosomal RNA
+Macromolecule #28: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S3Ae
+Macromolecule #5: 30S ribosomal protein S4
+Macromolecule #6: 30S ribosomal protein S4e
+Macromolecule #7: 30S ribosomal protein S5
+Macromolecule #8: 30S ribosomal protein S6e
+Macromolecule #9: 30S ribosomal protein S7
+Macromolecule #10: 30S ribosomal protein S8
+Macromolecule #11: 30S ribosomal protein S8e
+Macromolecule #12: 30S ribosomal protein S9
+Macromolecule #13: 30S ribosomal protein S10
+Macromolecule #14: 30S ribosomal protein S11
+Macromolecule #15: 30S ribosomal protein S12
+Macromolecule #16: 30S ribosomal protein S13
+Macromolecule #17: 30S ribosomal protein S15
+Macromolecule #18: 30S ribosomal protein S14 type Z
+Macromolecule #19: 30S ribosomal protein S17
+Macromolecule #20: 30S ribosomal protein S17e
+Macromolecule #21: 30S ribosomal protein S19
+Macromolecule #22: 30S ribosomal protein S19e
+Macromolecule #23: 30S ribosomal protein S24e
+Macromolecule #24: 30S ribosomal protein S27e
+Macromolecule #25: 30S ribosomal protein S28e
+Macromolecule #26: Predicted zinc-ribbon RNA-binding protein involved in translation
+Macromolecule #29: 50S ribosomal protein L2
+Macromolecule #30: 50S ribosomal protein L3
+Macromolecule #31: 50S ribosomal protein L4
+Macromolecule #32: 50S ribosomal protein L5
+Macromolecule #33: 50S ribosomal protein L6
+Macromolecule #34: 50S ribosomal protein L7Ae
+Macromolecule #35: 50S ribosomal protein L10e
+Macromolecule #36: 50S ribosomal protein L13
+Macromolecule #37: 50S ribosomal protein L14
+Macromolecule #38: 50S ribosomal protein L14e
+Macromolecule #39: 50S ribosomal protein L15
+Macromolecule #40: 50S ribosomal protein L15e
+Macromolecule #41: 50S ribosomal protein L18
+Macromolecule #42: 50S ribosomal protein L18e
+Macromolecule #43: 50S ribosomal protein L19e
+Macromolecule #44: 50S ribosomal protein L18Ae
+Macromolecule #45: 50S ribosomal protein L21e
+Macromolecule #46: 50S ribosomal protein L22
+Macromolecule #47: 50S ribosomal protein L23
+Macromolecule #48: 50S ribosomal protein L24
+Macromolecule #49: 50S ribosomal protein L24e
+Macromolecule #50: 50S ribosomal protein L29
+Macromolecule #51: 50S ribosomal protein L30
+Macromolecule #52: 50S ribosomal protein L30e
+Macromolecule #53: 50S ribosomal protein L31e
+Macromolecule #54: 50S ribosomal protein L32e
+Macromolecule #55: 50S ribosomal protein L34e
+Macromolecule #56: Ribosomal protein eL35A
+Macromolecule #57: 50S ribosomal protein L37Ae
+Macromolecule #58: 50S ribosomal protein L37e
+Macromolecule #59: 50S ribosomal protein L39e
+Macromolecule #60: 50S ribosomal protein L40e
+Macromolecule #61: LSU ribosomal protein L41E
+Macromolecule #62: 50S ribosomal protein L44e
+Macromolecule #63: Nucleic acid-binding protein, containing C2H2 zinc-finger
+Macromolecule #64: Predicted exosome subunit, UPF0023 family
+Macromolecule #65: Unknown ribosomal protein
+Macromolecule #66: ZINC ION
+Macromolecule #67: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 116585 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6skg: |