+Open data
-Basic information
Entry | Database: PDB / ID: 2lsn | ||||||
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Title | Solution structure of PFV RNase H domain | ||||||
Components | RNase HRibonuclease H | ||||||
Keywords | VIRAL PROTEIN / Rnase H | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / host cell / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / host cell / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human spumaretrovirus | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Leo, B. / Schweimer, K. / Woehrl, B. | ||||||
Citation | Journal: Retrovirology / Year: 2012 Title: The solution structure of the prototype foamy virus RNase H domain indicates an important role of the basic loop in substrate binding. Authors: Leo, B. / Schweimer, K. / Rosch, P. / Hartl, M.J. / Wohrl, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lsn.cif.gz | 929.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lsn.ent.gz | 781.8 KB | Display | PDB format |
PDBx/mmJSON format | 2lsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/2lsn ftp://data.pdbj.org/pub/pdb/validation_reports/ls/2lsn | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18056.520 Da / Num. of mol.: 1 / Fragment: UNP residues 591-751 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Gene: RNase H / Plasmid: pET-GB1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P14350 |
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Sequence details | AUTHORS STATE THAT THE SEQUENCE IS NOT 100% HOMOLOGOUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-13C; U-15N] PFV RNase H, 90 % H2O, 10 % D2O, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 120 / Conformers submitted total number: 19 |