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- PDB-6emo: Solution structure of the LEDGF/p75 IBD - JPO2 (aa 1-32) complex -

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Basic information

Entry
Database: PDB / ID: 6emo
TitleSolution structure of the LEDGF/p75 IBD - JPO2 (aa 1-32) complex
ComponentsPC4 and SFRS1-interacting protein,LEDGF/p75 IBD-JPO2 M1
KeywordsTRANSCRIPTION / 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 / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / 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 / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / euchromatin / fibrillar center / response to heat / response to oxidative stress / DNA-binding transcription factor binding / transcription coactivator activity / chromatin remodeling / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Zinc-finger domain of monoamine-oxidase A repressor R1 / CDCA7/CDA7L / Zinc-finger domain of monoamine-oxidase A repressor R1 / 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
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Cell division cycle-associated 7-like protein
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein,LEDGF/p75 IBD-JPO2 M1


Theoretical massNumber of molelcules
Total (without water)15,6951
Polymers15,6951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9440 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,LEDGF/p75 IBD-JPO2 M1 / 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


Mass: 15694.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75475, UniProt: Q96GN5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HMQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D C(CO)NH
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-JPO2 M1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O
Label: CN_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLEDGF/p75 IBD-JPO2 M1[U-13C; U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 200 mM / Label: c1 / pH: 7 / Pressure: arbitrary 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
NameClassification
TopSpinstructure solution
Sparkystructure solution
CYANAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
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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