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Yorodumi- PDB-5yi9: Solution structure of the LEDGF/p75 IBD - JPO2 (aa 56-91) complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yi9 | ||||||
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Title | Solution structure of the LEDGF/p75 IBD - JPO2 (aa 56-91) complex | ||||||
Components | PC4 and SFRS1-interacting protein,Cell division cycle-associated 7-like protein | ||||||
Keywords | TRANSCRIPTION / protein-protein complex / epigenetics / leukemia | ||||||
Function / homology | Function and homology information supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / euchromatin / fibrillar center / response to heat / DNA-binding transcription factor binding / transcription coactivator activity / response to oxidative stress / chromatin remodeling / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Veverka, V. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation. Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / ...Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / Christ, F. / Rezacova, P. / Hodges, H.C. / Debyser, Z. / Veverka, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yi9.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5yi9.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 5yi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yi9_validation.pdf.gz | 567 KB | Display | wwPDB validaton report |
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Full document | 5yi9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5yi9_validation.xml.gz | 96.8 KB | Display | |
Data in CIF | 5yi9_validation.cif.gz | 158.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yi9 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yi9 | HTTPS FTP |
-Related structure data
Related structure data | 6emoC 6empC 6emqC 6emrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: Protein | Mass: 16338.519 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 345-442,UNP RESIDUES 345-442 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2, CDCA7L, HR1, JPO2, R1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75475, UniProt: Q96GN5 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD- JPO2 M2, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O Label: s1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 200 mM / Label: c1 / pH: 7 / Pressure: arbitrary Pa / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 40 |