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Yorodumi- PDB-1fqz: NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL ... -
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-Basic information
Entry | Database: PDB / ID: 1fqz | ||||||
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Title | NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE | ||||||
Components | HEPATITIS C VIRUS IRES DOMAIN IIID | ||||||
Keywords | RNA / trans wobble G.U pair / S-turn / sarcin-ricin loop / loop E motif / sheared G.A pair / reverse Hoogsteen A.U pair | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data. | ||||||
Authors | Klinck, R. / Westhof, E. / Walker, S. / Afshar, M. / Collier, A. / Aboul-ela, F. | ||||||
Citation | Journal: RNA / Year: 2000 Title: A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. Authors: Klinck, R. / Westhof, E. / Walker, S. / Afshar, M. / Collier, A. / Aboul-Ela, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fqz.cif.gz | 25.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fqz.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fqz ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fqz | HTTPS FTP |
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-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: 8800.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Transcribed 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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-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S- ...Method: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data. Software ordinal: 1 Details: Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy Conformers calculated total number: 1 / Conformers submitted total number: 1 |