[English] 日本語
Yorodumi- PDB-8oeq: Crystal structure of the Candida albicans 80S ribosome in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oeq | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the Candida albicans 80S ribosome in complex with Paromomycin (250uM) | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | RIBOSOME / Candida albicans / paromomycin | ||||||||||||||||||
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 / protein tag activity / rRNA processing / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / 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: 3.3 Å | ||||||||||||||||||
Authors | Kolosova, O. / Zgadzay, Y. / Yusupov, M. | ||||||||||||||||||
Funding support | France, Russian Federation, United States, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published Title: Drug-induced rotational movement of the ribosome is a key factor for read-through enhancement Authors: Kolosova, O. / Zgadzay, Y. / Stetsenko, A. / Validov, S. / Usachev, K. / Jenner, L. / Dmitriev, S. / Guskov, A. / Yusupov, M. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oeq.cif.gz | 10 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oeq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8oeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oeq_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8oeq_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 8oeq_validation.xml.gz | 1 MB | Display | |
Data in CIF | 8oeq_validation.cif.gz | 1.5 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oeq ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oeq | HTTPS FTP |
-Related structure data
Related structure data | 8cq7C 8cqwC 8creC 8ogjC 8oh6C 8oi5C 8oj3C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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) / References: GenBank: XR_002086444.1 #2: RNA chain | Mass: 38943.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: X16634.1 #3: RNA chain | Mass: 50683.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: OQ195134.1 #46: RNA chain | Mass: 575838.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086442.1 |
---|
+60S ribosomal protein ... , 37 types, 74 molecules jAWkAXlAYnBAoBBpBCqBDrBEsBFtBGuBHvBIyBLzBM0BN...
-Protein , 4 types, 8 molecules mAZhDSARDTL1l1
#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: 24416.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4E7 |
---|
-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 |
---|
+40S ribosomal protein ... , 25 types, 50 molecules CCNDCOGCRICTJCUKCVMCXNCYOCZPDAQDBRDCSDDTDEUDF...
-Non-polymers , 5 types, 1524 molecules
#81: Chemical | ChemComp-MG / #82: Chemical | #83: Chemical | ChemComp-PAR / #84: Chemical | ChemComp-ZN / #85: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.1 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 20K, KSCN, Mg Acetate, K - acetate, Bis-Tris-Acetate, Glycerol, Spermidine, phyllanthoside |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→177.03 Å / Num. obs: 1134400 / % possible obs: 99.3 % / Redundancy: 14.4 % / Biso Wilson estimate: 87.83 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.695 / Rpim(I) all: 0.1885 / Rrim(I) all: 0.721 / Net I/σ(I): 4.36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→177.03 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.43 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→177.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|