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- PDB-1ju7: NMR Solution Structure of the RNA Hairpin Binding Site for the Hi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ju7 | ||||||||||||||||||
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Title | NMR Solution Structure of the RNA Hairpin Binding Site for the Histone Stem-loop Binding Protein | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / hairpin / tetraloop / 3' stack | Function / homology | : / RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / simulated annealing, molecular dynamics | ![]() DeJong, E.S. / Marzluff, W.F. / Nikonowicz, E.P. | ![]() ![]() Title: NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein. Authors: DeJong, E.S. / Marzluff, W.F. / Nikonowicz, E.P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 84.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 326 KB | Display | ![]() |
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Full document | ![]() | 386.4 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 8928.382 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally at the 3' end of the replication-dependent histone mRNAs of vertebrates. This sequence corresponds to the mouse H4-12 gene. References: GenBank: 51308 |
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-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 a variety of 2D and 3D homo- and hetero-nuclear NMR methods. |
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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 | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: Calculations were performed using 232 conformationally restrictive NOE derived distance constraints and 55 backbone and 15 ribose torsion angle constraints. Base pair constraints were ...Details: Calculations were performed using 232 conformationally restrictive NOE derived distance constraints and 55 backbone and 15 ribose torsion angle constraints. Base pair constraints were introduced for six base pairs using heavy atom-heavy atom constraints. Coordinates are for the hairpin domain only. 5' flanking (ggccaaa) and 3' flanking (accca) coordinates are not included with this deposition. Few constraints were obtained for these very dynamic regions and although they were included as part of the structure calculation, their conformations appear to be randomly distributed. | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 60 / Conformers submitted total number: 10 |