+Open data
-Basic information
Entry | Database: PDB / ID: 1p5o | ||||||
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Title | Solution Structure of HCV IRES Domain II | ||||||
Components | 77-MER | ||||||
Keywords | RNA / RIBONUCLEIC ACID / HEPATITIS C VIRUS / INTERNAL RIBOSOME ENTRY SITE / tRNA / LOOP E MOTIF / HAIRPIN LOOP | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / see reference above | ||||||
Authors | Lukavsky, P.J. / Kim, I. / Otto, G.A. / Puglisi, J.D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of HCV IRES domain II determined by NMR. Authors: Lukavsky, P.J. / Kim, I. / Otto, G.A. / Puglisi, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p5o.cif.gz | 563.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p5o.ent.gz | 479.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p5o_validation.pdf.gz | 314.1 KB | Display | wwPDB validaton report |
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Full document | 1p5o_full_validation.pdf.gz | 401.7 KB | Display | |
Data in XML | 1p5o_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1p5o_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p5o ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p5o | HTTPS FTP |
-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: 24776.691 Da / Num. of mol.: 1 / Fragment: HCV IRES domain II (residues 45-117) / Source method: obtained synthetically Details: Synthesized by in vitro transcription from linearized plasmid DNA using T7 RNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings |
-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: see reference above / Software ordinal: 1 / Details: see reference above | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: lowest restraint violation and total energy Conformers calculated total number: 200 / Conformers submitted total number: 12 |