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- PDB-6emp: Solution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex -

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Basic information

Entry
Database: PDB / ID: 6emp
TitleSolution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex
ComponentsPC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain
KeywordsTRANSCRIPTION / protein-protein complex / epigenetics / leukemia
Function / homology
Function and homology information


kinetochore assembly / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / mitotic sister chromatid cohesion / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus ...kinetochore assembly / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / mitotic sister chromatid cohesion / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / euchromatin / double-strand break repair via homologous recombination / response to heat / response to oxidative stress / DNA-binding transcription factor binding / transcription coactivator activity / ciliary basal body / chromatin remodeling / cell division / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Z280C/D-like C2H2 zinc finger / POGZ-like double zinc finger / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / : / Lens epithelium-derived growth factor, integrase-binding domain ...Z280C/D-like C2H2 zinc finger / POGZ-like double zinc finger / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / : / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Pogo transposable element with ZNF domain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVeverka, V.
CitationJournal: 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
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain


Theoretical massNumber of molelcules
Total (without water)16,0361
Polymers16,0361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Suppressor of hairy wing homolog 5 / Zinc finger protein 280E / Zinc finger protein 635


Mass: 16036.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: PSIP1, DFS70, LEDGF, PSIP2, POGZ, KIAA0461, SUHW5, ZNF280E, ZNF635, Nbla00003
Production host: Escherichia coli (E. coli) / References: UniProt: O75475, UniProt: Q7Z3K3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HNCO
131isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-POGZ, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLEDGF/p75 IBD-POGZ[U-13C; U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 200 mM / Label: c1 / pH: 7 / Pressure: arbitraty Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKriegerrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40

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