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Yorodumi- PDB-2n3a: Solution structure of LEDGF/p75 IBD in complex with POGZ peptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n3a | ||||||
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Title | Solution structure of LEDGF/p75 IBD in complex with POGZ peptide (1389-1404) | ||||||
Components |
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Keywords | PROTEIN BINDING / LEDGF/p75 / PogZ / H3K36me3 | ||||||
Function / homology | Function and homology information kinetochore assembly / supercoiled DNA binding / mitotic sister chromatid cohesion / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection ...kinetochore assembly / supercoiled DNA binding / mitotic sister chromatid cohesion / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / double-strand break repair via homologous recombination / euchromatin / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell division / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | ||||||
Authors | Tesina, P. / Cermakova, K. / Horejsi, M. / Prochazkova, K. / Fabry, M. / Sharma, S. / Christ, F. / Demeulemeester, J. / Debyser, Z. / De Rijck, J. ...Tesina, P. / Cermakova, K. / Horejsi, M. / Prochazkova, K. / Fabry, M. / Sharma, S. / Christ, F. / Demeulemeester, J. / Debyser, Z. / De Rijck, J. / Veverka, V. / Rezacova, P. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif. Authors: Tesina, P. / Cermakova, K. / Horejsi, M. / Prochazkova, K. / Fabry, M. / Sharma, S. / Christ, F. / Demeulemeester, J. / Debyser, Z. / Rijck, J.D. / Veverka, V. / Rezacova, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n3a.cif.gz | 877.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n3a.ent.gz | 768.4 KB | Display | PDB format |
PDBx/mmJSON format | 2n3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/2n3a ftp://data.pdbj.org/pub/pdb/validation_reports/n3/2n3a | 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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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1825.748 Da / Num. of mol.: 1 / Fragment: UNP residues 1389-1404 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z3K3 |
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#2: Protein | Mass: 9355.052 Da / Num. of mol.: 1 / Fragment: UNP residues 348-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Plasmid: pET / References: UniProt: O75475 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM peptide, 0.5 mM [U-13C; U-15N] protein, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 125 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, molecular dynamics / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 29 |