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Yorodumi- PDB-2l4l: Structural insights into the cTAR DNA recognition by the HIV-1 Nu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l4l | ||||||
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Title | Structural insights into the cTAR DNA recognition by the HIV-1 Nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC | ||||||
Components |
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Keywords | VIRAL PROTEIN/DNA / NC(11-55):mini-cTAR / VIRAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Bazzi, A. / Zargarian, L. / Chaminade, F. / Boudier, C. / De Rocquigny, H. / Rene, B. / Mely, Y. / Fosse, P. / Mauffret, O. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC. Authors: Bazzi, A. / Zargarian, L. / Chaminade, F. / Boudier, C. / De Rocquigny, H. / Rene, B. / Mely, Y. / Fosse, P. / Mauffret, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l4l.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l4l.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 2l4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/2l4l ftp://data.pdbj.org/pub/pdb/validation_reports/l4/2l4l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5152.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P03366*PLUS | ||
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#2: DNA chain | Mass: 1206.829 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM HIV-1 nucleocapsid protein NCp7(11-55)-1, 1 mM DNA, 10 % D2O-3, 90 % H2O-4, 3 mM RZN-5, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry 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: 50 / Conformers submitted total number: 10 / Representative conformer: 5 |