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Yorodumi- PDB-8c3a: Crystal structure of ailanthone bound to the Candida albicans 80S... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 8c3a | ||||||||||||||||||
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| Title | Crystal structure of ailanthone bound to the Candida albicans 80S ribosome | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / Candida albicans / ailanthone | ||||||||||||||||||
| Function / homology | Function and homology informationnegative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / GCN2-mediated signaling / hyphal cell wall / triplex DNA binding / ribosome hibernation / preribosome / translation elongation factor binding ...negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / regulation of cytoplasmic translation / GCN2-mediated signaling / hyphal cell wall / triplex DNA binding / ribosome hibernation / preribosome / translation elongation factor binding / negative regulation of p38MAPK cascade / regulation of translational initiation in response to stress / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / nonfunctional rRNA decay / preribosome, small subunit precursor / telomeric DNA binding / mRNA destabilization / negative regulation of translational frameshifting / TOR signaling / negative regulation of mRNA splicing, via spliceosome / signaling receptor activator activity / translational elongation / G-protein alpha-subunit binding / 90S preribosome / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / protein-membrane adaptor activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of autophagy / rescue of stalled ribosome / telomere maintenance / ribosomal large subunit biogenesis / 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) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / cell surface / RNA binding / extracellular region / zinc ion binding / metal ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
| Biological species | Candida albicans (yeast) | ||||||||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||||||||
Authors | Kolosova, O. / Zgadzay, Y. / Yusupov, M. | ||||||||||||||||||
| Funding support | France, Russian Federation, United States, 5items
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Citation | Journal: To Be PublishedTitle: New crystal system to promote screening for new eukaryotic inhibitors Authors: Kolosova, O. / Zgadzay, Y. / Wu, C. / Validov, S. / Usachev, K. / Jenner, L. / Sachs, M.S. / Yusupova, G. / Yusupov, M. | ||||||||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8c3a.cif.gz | 10.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb8c3a.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 8c3a.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8c3a_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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| Full document | 8c3a_full_validation.pdf.gz | 2.7 MB | Display | |
| Data in XML | 8c3a_validation.xml.gz | 949.4 KB | Display | |
| Data in CIF | 8c3a_validation.cif.gz | 1.4 MB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/8c3a ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c3a | HTTPS FTP |
-Related structure data
| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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Components
-RNA chain , 4 types, 8 molecules 1AS3AT4AUBCM
| #1: RNA chain | Mass: 1085278.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)#2: RNA chain | Mass: 38943.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)#3: RNA chain | Mass: 50683.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)#46: RNA chain | Mass: 575838.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) |
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+60S ribosomal protein ... , 38 types, 75 molecules jAWkAXlAYnBAoBBpBCqBDrBEsBFtBGuBHvBIyBLzBM0BN...
-Protein , 5 types, 10 molecules mAZhDSARDTP0p0L1l1
| #7: Protein | Mass: 34557.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UAA6#78: Protein | Mass: 22615.525 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109#79: Protein | Mass: 34593.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3E7#80: Protein | Mass: 33302.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: G1UA71#82: Protein | Mass: 24416.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4E7 |
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-Ribosomal protein ... , 10 types, 20 molecules wBJxBK9BTAICCECPFCQHCSLCWWDHZDK
| #17: Protein | Mass: 22685.850 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ56#18: Protein | Mass: 21002.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BUG0#27: Protein | Mass: 14215.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3X2#36: Protein | Mass: 14118.759 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6B7#49: Protein | Mass: 26917.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ90#50: Protein | Mass: 27313.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYS1#52: Protein | Mass: 25319.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BS29#56: Protein | Mass: 21765.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X2#67: Protein | Mass: 13366.540 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYJ9#70: Protein | Mass: 16000.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V0 |
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+40S ribosomal protein ... , 25 types, 50 molecules CCNDCOGCRICTJCUKCVMCXNCYOCZPDAQDBRDCSDDTDEUDF...
-Non-polymers , 5 types, 1518 molecules 








| #83: Chemical | ChemComp-MG / #84: Chemical | #85: Chemical | #86: Chemical | ChemComp-ZN / #87: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.41 % |
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| Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 20000, potassium acetate, potassium thiocyanate, magnesium acetate, bis-tris, spermidine |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 3→227.5 Å / Num. obs: 1514598 / % possible obs: 99.4 % / Redundancy: 21.6 % / CC1/2: 0.994 / Rrim(I) all: 0.759 / Net I/σ(I): 4.81 |
| Reflection shell | Resolution: 3→3.1 Å / Num. unique obs: 73124 / CC1/2: 0.04 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→227.46 Å / SU ML: 0.93 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.87 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3→227.46 Å
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| Refine LS restraints |
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| LS refinement shell |
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About Yorodumi



Candida albicans (yeast)
X-RAY DIFFRACTION
France,
Russian Federation,
United States, 5items
Citation
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