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- PDB-1z9e: Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75 -

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Basic information

Entry
Database: PDB / ID: 1z9e
TitleSolution structure of the HIV-1 integrase-binding domain in LEDGF/p75
ComponentsPC4 and SFRS1 interacting protein 2
KeywordsPROTEIN BINDING/TRANSCRIPTION / HEAT repeat-like / LEDGF / PROTEIN BINDING-TRANSCRIPTION COMPLEX
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
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCherepanov, P. / Sun, Z.-Y.J. / Rahman, S. / Maertens, G. / Wagner, G. / Engelman, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75
Authors: Cherepanov, P. / Sun, Z.-Y.J. / Rahman, S. / Maertens, G. / Wagner, G. / Engelman, A.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PC4 and SFRS1 interacting protein 2


Theoretical massNumber of molelcules
Total (without water)14,6291
Polymers14,6291
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)15 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein PC4 and SFRS1 interacting protein 2


Mass: 14628.919 Da / Num. of mol.: 1
Fragment: sequence database residues 347-471 contains: HIV-1 integrase-binding domain (residues 347-429)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / 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
2122D NOESY
1213D 15N-separated NOESY
2323D 13C-separated NOESY
141HNCA, HN(CO)CA, HNCO, HN(CA)CO, HN(CA)CB, HN(CO)CACB, H(CCO)NH, C(CO)NH
252(H)CCH-TOCSY
NMR detailsText: the structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM protein, 100 mM NaCl, 50 mM Phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
20.7 mM protein, 100 mM NaCl, 38 mM Na2HPO4, 12 mM NaH2PO4, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM NaCl, 50 mM Posphate buffer / pH: 7.25 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7501
Bruker AVANCEBrukerAVANCE6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.structure solution
X-PLOR3.851Brunger, A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 15

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