+Open data
-Basic information
Entry | Database: PDB / ID: 1f85 | ||||||
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Title | SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIIE | ||||||
Components | HCV-1B IRES RNA DOMAIN IIIE | ||||||
Keywords | RNA / Ribonucleic Acid / Hepatitis C virus internal ribosome entry site / Hairpin loop / Tetraloop / RNA structure | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / Simulated annealing, restrained molecular dynamics | ||||||
Authors | Lukavsky, P.J. / Otto, G.A. / Lancaster, A.M. / Sarnow, P. / Puglisi, J.D. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. Authors: Lukavsky, P.J. / Otto, G.A. / Lancaster, A.M. / Sarnow, P. / 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 | 1f85.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f85.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 1f85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f85 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f85 | 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: 4518.731 Da / Num. of mol.: 1 Fragment: HCV IRES RNA DOMAIN IIIE (NUCLEOTIDES 290-303 OF GENOMIC HEPATITIS C VIRAL RNA) Mutation: U290G, G303C / Source method: obtained synthetically Details: Synthesized enzymatically in-vitro using T7 RNA Polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 31P-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY |
NMR details | Text: THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. NATURAL ABUNDANCE 13C HMQC EXPERIMENTS WERE PERFORMED. |
-Sample preparation
Details | Contents: 2.5mM RNA, non-isotopically labelled Solvent system: sodium phosphate buffer, 96% H2O/4% D2O or 100% D2O |
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Sample conditions | Ionic strength: 10mM / pH: 6.40 / Pressure: ambient / Temperature: 283 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing, restrained molecular dynamics / Software ordinal: 1 / Details: SEE REFERENCE ABOVE | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |