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Yorodumi- PDB-1lpw: Solution structure of the yeast spliceosomal U2 snRNA-intron bran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpw | ||||||
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Title | Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine | ||||||
Components |
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Keywords | RNA / U2 snRNA / branch site / pseudouridine | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / torsion angle molecular dynamics, conjugate gradient minimization | ||||||
Authors | Newby, M.I. / Greenbaum, N.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine Authors: Newby, M.I. / Greenbaum, N.L. | ||||||
History |
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Remark 999 | SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds ...SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds to position 5 on strand A, which is a uridine in 1LMV, and a pseudouridine in 1LPW. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpw.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpw.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpw ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpw | 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: RNA chain | Mass: 2912.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: U2 snRNA / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#2: RNA chain | Mass: 3104.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: pre-mRNA conserved intron branch site sequence site Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to ...Text: This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to resolve some spectral overlap. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-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: torsion angle molecular dynamics, conjugate gradient minimization Software ordinal: 1 Details: A total of 191 distance restraints were used, not including the 40 hydrogen bond distances imposed. Including the 133 dihedral restraints applied in structure calculations, 353 total restraints were applied. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy structure that agreed best with experimental data | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: lowest energy structures that did not violate data from fluorescence experiments Conformers calculated total number: 800 / Conformers submitted total number: 9 |