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Yorodumi- PDB-8c3a: Crystal structure of ailanthone bound to the Candida albicans 80S... -
+Open data
-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 information yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation ...yeast-form cell wall / hyphal cell wall / triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / pre-mRNA 5'-splice site binding / telomeric DNA binding / negative regulation of mRNA splicing, via spliceosome / translational elongation / TOR signaling / protein-RNA complex assembly / ribosomal subunit export from nucleus / translation regulator activity / translation repressor activity / maturation of LSU-rRNA / cytosolic ribosome / telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / ubiquitin protein ligase binding / negative regulation of apoptotic process / cell surface / RNA binding / zinc ion binding / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm 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 Published Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-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 & homologyF&H Search |
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-Links
-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 |
-Processing
Software |
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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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