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Yorodumi- PDB-1y2y: Structural Characterization of Nop10p using Nuclear Magnetic Reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y2y | ||||||
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Title | Structural Characterization of Nop10p using Nuclear Magnetic Resonance Spectroscopy | ||||||
Components | Ribosome biogenesis protein Nop10 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Box H/ACA snoRNA / snoRNP / pseudouridine | ||||||
Function / homology | Function and homology information snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / snRNA pseudouridine synthesis / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / snoRNA binding / rRNA processing / nucleolus / RNA binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / refinement with simulated annealing | ||||||
Authors | Khanna, M. / Wu, H. / Johansson, C. / Caizergues-Ferrer, M. / Feigon, J. | ||||||
Citation | Journal: RNA / Year: 2006 Title: Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA Authors: Khanna, M. / Wu, H. / Johansson, C. / Caizergues-Ferrer, M. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y2y.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y2y.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 1y2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/1y2y ftp://data.pdbj.org/pub/pdb/validation_reports/y2/1y2y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6649.745 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NOP10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q6Q547 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 110 mM / pH: 6.5 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: refinement with simulated annealing / Software ordinal: 1 Details: The structures are based on 354 intraresidue NOEs, 191 sequential NOES and 10 hydrogen bond restraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 10 |