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Yorodumi- PDB-6skg: Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 dele... -
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-Basic information
Entry | Database: PDB / ID: 6skg | |||||||||
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Title | Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain | |||||||||
Components |
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Keywords | RIBOSOME / T. kodakarensis / ac4C deletion / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 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 / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Matzov, D. / Sas-Chen, A. / Thomas, J.M. / Santangelo, T. / Meier, J.L. / Schwartz, S. / Shalev-Benami, M. | |||||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6skg.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6skg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6skg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6skg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6skg_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6skg_validation.xml.gz | 280.3 KB | Display | |
Data in CIF | 6skg_validation.cif.gz | 483.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6skg ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6skg | HTTPS FTP |
-Related structure data
Related structure data | 10224MC 6skfC 6th6C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules AaBABB
#1: RNA chain | Mass: 487394.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
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#27: RNA chain | Mass: 987981.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
#28: RNA chain | Mass: 40744.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: GenBank: 57158259 |
+30S ribosomal protein ... , 24 types, 26 molecules AbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtBmAuAvAwBnAxAy
-Protein , 3 types, 3 molecules AzBfBp
#26: Protein | Mass: 7001.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JFE2 |
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#56: Protein | Mass: 11064.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
#64: Protein | Mass: 26873.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIV0 |
+50S ribosomal protein ... , 32 types, 34 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBg...
-Protein/peptide , 3 types, 3 molecules BkBoBq
#61: Protein/peptide | Mass: 5051.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JEV0 |
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#63: Protein/peptide | Mass: 5485.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JFH3 |
#65: Protein/peptide | Mass: 2434.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
-Non-polymers , 2 types, 3570 molecules
#66: Chemical | ChemComp-ZN / #67: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 70S ribosome from Thermococcus kodakarensis / Type: RIBOSOME / Entity ID: #1-#65 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 29000 X / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 34 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116585 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |