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- PDB-3zeh: Solution structure of the Hs. PSIP1 PWWP domain -

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Basic information

Entry
Database: PDB / ID: 3zeh
TitleSolution structure of the Hs. PSIP1 PWWP domain
ComponentsPC4 AND SFRS1-INTERACTING PROTEIN
KeywordsDNA 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 / CYANA, WATER-REFINEMENT IN CNS
Authorsvan Ingen, H. / van Nuland, R. / Timmers, H.T.M. / Boelens, R.
CitationJournal: Epigenetics Chromatin / Year: 2013
Title: Nucleosomal DNA Binding Drives the Recognition of H3K36-Methylated Nucleosomes by the Psip1-Pwwp Domain.
Authors: Van Nuland, R. / Van Schaik, F.M. / Simonis, M. / Van Heesch, S. / Cuppen, E. / Boelens, R. / Timmers, H.T.M. / Van Ingen, H.
History
DepositionDec 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)11,9041
Polymers11,9041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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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 / PSIP1


Mass: 11903.595 Da / Num. of mol.: 1 / Fragment: PWWP DOMAIN, RESIDUES 3-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O75475

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
12113C/15N EDITED NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER 10% D2O 20 MM NAPI PH 6 100 MM NACL
Sample conditionsIonic strength: 100 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
CYANAstructure solution
CNSstructure solution
RefinementMethod: CYANA, WATER-REFINEMENT IN CNS / Software ordinal: 1
Details: REFINEMENT IN EXPLICIT WATER USING RECOORD PROTOCOL
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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