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Yorodumi- PDB-2luq: Solution structure of double-stranded RNA binding domain of S.cer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2luq | ||||||
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Title | Solution structure of double-stranded RNA binding domain of S.cerevisiae RNase III (rnt1p) | ||||||
Components | Ribonuclease 3 | ||||||
Keywords | RNA BINDING PROTEIN / DSRBD / RNT1P | ||||||
Function / homology | Function and homology information box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription ...box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Wang, Z. / Feigon, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Intrinsic Dynamics of an Extended Hydrophobic Core in the S. cerevisiae RNase III dsRBD Contributes to Recognition of Specific RNA Binding Sites. Authors: Hartman, E. / Wang, Z. / Zhang, Q. / Roy, K. / Chanfreau, G. / Feigon, J. #1: Journal: Structure / Year: 2011 Title: Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs. Authors: Wang, Z. / Hartman, E. / Roy, K. / Chanfreau, G. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2luq.cif.gz | 543.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2luq.ent.gz | 459.5 KB | Display | PDB format |
PDBx/mmJSON format | 2luq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/2luq ftp://data.pdbj.org/pub/pdb/validation_reports/lu/2luq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9822.364 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RNT1, YM9408.01C, YM9959.21, YMR239C / Variant: YMR239C / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q02555 |
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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 |
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Sample conditions | Ionic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1859 / NOE intraresidue total count: 585 / NOE long range total count: 410 / NOE medium range total count: 420 / NOE sequential total count: 444 | ||||||||||||||||||||||||||||
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 |