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- PDB-2m16: P75/LEDGF PWWP Domain -

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Basic information

Entry
Database: PDB / ID: 2m16
TitleP75/LEDGF PWWP Domain
ComponentsPC4 and SFRS1-interacting protein
KeywordsTRANSCRIPTION / protein / PWWP domain / DNA binding
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 / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCrowe, B.L. / Foster, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes.
Authors: Eidahl, J.O. / Crowe, B.L. / North, J.A. / McKee, C.J. / Shkriabai, N. / Feng, L. / Plumb, M. / Graham, R.L. / Gorelick, R.J. / Hess, S. / Poirier, M.G. / Foster, M.P. / Kvaratskhelia, M.
History
DepositionNov 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 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


Theoretical massNumber of molelcules
Total (without water)11,0321
Polymers11,0321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150target function
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: 11031.594 Da / Num. of mol.: 1 / Fragment: unp residues 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DFS70, LEDGF, PSIP1, PSIP2 / Plasmid: pFT-1-LEDGF / 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-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aromatic
1312D 1H-13C HSQC aliphatic
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CC(CO)NH-TOCSY
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.35-0.45 mM [U-99% 13C; U-99% 15N] entity, 50 mM HEPES, 150 mM sodium chloride, 2 mM beta-mercaptoethanol, 0.66 mM DSS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-99% 13C; U-99% 15N]0.35-0.451
50 mMHEPES-21
150 mMsodium chloride-31
2 mMbeta-mercaptoethanol-41
0.66 mMDSS-51
Sample conditionsIonic strength: 0.35 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TALOS+Cornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJ9.0.0-b44Johnson, One Moon Scientificchemical shift assignment
NMRViewJ9.0.0-b44Johnson, One Moon Scientificpeak picking
XwinNMRBruker Biospincollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1439 / NOE intraresidue total count: 302 / NOE long range total count: 471 / NOE medium range total count: 245 / NOE sequential total count: 421
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 10.9 ° / Maximum upper distance constraint violation: 0.23 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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