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Yorodumi- PDB-2p89: Solution structure of the 3' pseudouridyation pocket of U65 snoRN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p89 | ||||||
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Title | Solution structure of the 3' pseudouridyation pocket of U65 snoRNA with bound substrate | ||||||
Components |
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Keywords | RNA / RNA-RNA complex / three-way junctions / double helix | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing | ||||||
Authors | Wu, H. / Feigon, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Authors: Wu, H. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p89.cif.gz | 586.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p89.ent.gz | 494.9 KB | Display | PDB format |
PDBx/mmJSON format | 2p89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p89_validation.pdf.gz | 329.7 KB | Display | wwPDB validaton report |
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Full document | 2p89_full_validation.pdf.gz | 578.9 KB | Display | |
Data in XML | 2p89_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 2p89_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/2p89 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/2p89 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 10970.566 Da / Num. of mol.: 1 / Fragment: 3' pseudouridylation pocket Mutation: Additional UUCG tetraloop and G:C base pair at the end the helices Source method: obtained synthetically / Details: This sequence occurs naturally in humans |
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#2: RNA chain | Mass: 4337.563 Da / Num. of mol.: 1 / Fragment: fragment 4423-4436 / Mutation: G4423U / Source method: obtained synthetically / Details: This sequence occurs naturally in humans |
-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: 5 mM / pH: 6 / 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: distance geometry simulated annealing / Software ordinal: 1 Details: the structures are based on 768 NOE-derived distance constraints, 404 dihedral angle restraints,106 distance restraints from hydrogen bonds, 32 RDC restraints | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |