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- PDB-6tvm: LEDGF/p75 dimer (residues 345-467) -

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Basic information

Entry
Database: PDB / ID: 6tvm
TitleLEDGF/p75 dimer (residues 345-467)
ComponentsPC4 and SFRS1-interacting protein
KeywordsTRANSCRIPTION / epigenetic reader / integrase-binding domain / domain-swapped dimer
Function / homology
Function and homology information


supercoiled DNA binding / 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 ...supercoiled DNA binding / 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 / euchromatin / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / chromatin binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLux, V. / Veverka, V.
CitationJournal: Structure / Year: 2020
Title: Molecular Mechanism of LEDGF/p75 Dimerization.
Authors: Lux, V. / Brouns, T. / Cermakova, K. / Srb, P. / Fabry, M. / Madlikova, M. / Horejsi, M. / Kukacka, Z. / Novak, P. / Kugler, M. / Brynda, J. / DeRijck, J. / Christ, F. / Debyser, Z. / Veverka, V.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PC4 and SFRS1-interacting protein
B: PC4 and SFRS1-interacting protein


Theoretical massNumber of molelcules
Total (without water)29,2902
Polymers29,2902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6280 Å2
ΔGint-45 kcal/mol
Surface area17300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein PC4 and SFRS1-interacting protein / 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: 14644.854 Da / Num. of mol.: 2
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

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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 HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LEDGF, 20 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O
Label: cn / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLEDGF[U-13C; U-15N]1
20 mMHEPESnatural abundance1
100 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 120 mM / Label: cn1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
SparkyGoddarddata analysis
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / 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: 30

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