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3zeh

Solution structure of the Hs. PSIP1 PWWP domain

Method: SOLUTION NMR Dmax: 47.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PC4 AND SFRS1-INTERACTING PROTEIN

HOMO SAPIENS

UniProt O75475

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 3–100 Fragment：PWWP DOMAIN, RESIDUES 3-100 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR sample composition：90% WATER 10% D2O 20 MM NAPI PH 6 100 MM NACL Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3ZEH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Z9E Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75 Deposited 2005-04-01 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 347–471（125 aa） Fragment：sequence database residues 347-471 contains: HIV-1 integrase-binding domain (residues 347-429)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.25；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl, 50 mM Posphate buffer；Pressure ambient
NMR sample composition 0.7 mM protein, 100 mM NaCl, 50 mM Phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM protein, 100 mM NaCl, 38 mM Na2HPO4, 12 mM NaH2PO4, 100% D2O | 100% D2O
Resolution not provided
2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 347–442（96 aa） Fragment：LEDGF
Chain D 347–442（96 aa） Fragment：LEDGF
Not recorded PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.02 Å R-free 0.226
2B4J Structural basis for the recognition between HIV-1 integrase and LEDGF/p75 Deposited 2005-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 347–442（96 aa） Fragment：LEDGF
Chain D 347–442（96 aa） Fragment：LEDGF
Not recorded PO4 PHOSPHATE ION × 4 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；295 K；PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.02 Å R-free 0.226
2M16 P75/LEDGF PWWP Domain Deposited 2012-11-18 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–93（93 aa） Fragment：unp residues 1-93
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.35；Pressure ambient
NMR sample composition 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 | 95% H2O/5% D2O
Resolution not provided
2MSR Solution structure of LEDGF/p75 IBD in complex with MLL1 peptide (140-160) Deposited 2014-08-05 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 344–426（83 aa） Fragment：UNP residues 344-425
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition 0.5 mM MLL1_140, 0.5 mM [U-13C; U-15N] IBD, 25 mM HEPES, 100 mM sodium chloride, 0.05 % beta-mercaptoethanol, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MTN Solution structure of MLL-IBD complex Deposited 2014-08-23 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 337–442（106 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N3A Solution structure of LEDGF/p75 IBD in complex with POGZ peptide (1389-1404) Deposited 2015-05-26 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 348–426（79 aa） Fragment：UNP residues 348-426
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition 0.5 mM peptide, 0.5 mM [U-13C; U-15N] protein, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain m 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain q 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain u 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 13 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain W 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain i 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 14 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain K 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain a 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 15 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain m 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain q 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain u 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 16 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain O 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain S 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Chain e 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain W 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain a 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain e 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3F9K Two domain fragment of HIV-2 integrase in complex with LEDGF IBD Deposited 2008-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain i 347–435（89 aa） Fragment：LEDGF, Integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.234
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain H 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain K 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain L 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain J 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain K 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain L 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain H 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain I 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Chain J 347–435（89 aa） Fragment：integrase binding domain, UNP residues 347-435
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.28 Å R-free 0.253
3HPH Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD Deposited 2009-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435
Chain F 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435
Chain G 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435
Chain H 348–435（88 aa） Fragment：Integrase binding domain, UNP residues 348-435
Not recorded ZN ZINC ION × 4 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.64 Å R-free 0.253
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 347–435（89 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 4 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 347–435（89 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 1 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
4FU6 Crystal structure of the PSIP1 PWWP domain Deposited 2012-06-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–135（135 aa） Fragment：UNP residues 1-135
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；The protein sample was treated with V8 protease. 2.5M ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, temperature 291K
Resolution 2.10 Å R-free 0.232
5N88 Crystal structure of antibody bound to viral protein Deposited 2017-02-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 347–424（78 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25.0% PEG 3350, 10mM Tris pH8.5
Resolution 1.70 Å R-free 0.252
5N88 Crystal structure of antibody bound to viral protein Deposited 2017-02-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 347–425（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；25.0% PEG 3350, 10mM Tris pH8.5
Resolution 1.70 Å R-free 0.252
5OYM HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor Deposited 2017-09-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 345–431（87 aa）
Chain B 345–431（87 aa）
Chain C 345–431（87 aa）
Chain D 345–431（87 aa）
Chain E 345–431（87 aa）
Chain F 345–431（87 aa）
Chain G 345–431（87 aa）
Chain H 345–431（87 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Sodium Fluoride, 0.1 M bis-Tris propane, pH 8.5 and 20 % w/v PEG 3350
Resolution 2.05 Å R-free 0.236
5YI9 Solution structure of the LEDGF/p75 IBD - JPO2 (aa 56-91) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–442（98 aa） Fragment：UNP RESIDUES 345-442,UNP RESIDUES 345-442
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD- JPO2 M2, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6EMO Solution structure of the LEDGF/p75 IBD - JPO2 (aa 1-32) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–442（98 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-JPO2 M1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6EMP Solution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–442（98 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitraty
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-POGZ, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6EMQ Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–443（99 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6EMR Solution structure of the LEDGF/p75 IBD - IWS1 (aa 446-548) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–441（97 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-IWS1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.20 Å
6TRJ LEDGF/p75 IBD dimer Deposited 2019-12-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 345–430（86 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 (Morpheus Molecular Dimensions condition H11)
Resolution 1.30 Å R-free 0.177
6TVM LEDGF/p75 dimer (residues 345-467) Deposited 2020-01-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 345–467（123 aa）
Chain B 345–467（123 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure 1
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF, 20 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6ZV0 TFIIS N-terminal domain (TND) from human LEDGF/p75 Deposited 2020-07-23 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 345–431（87 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 225；Pressure 1
NMR sample composition 0.6 mM [U-13C; U-15N] LEDGF/p75, 25 mM [U-2H] TRIS, 200 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7OUF Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450 Deposited 2021-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–325（325 aa）
Chain F 1–325（325 aa）
Not recorded ZN ZINC ION × 4 MG MAGNESIUM ION × 4 1L0 4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OUG STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir Deposited 2021-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–325（325 aa）
Chain F 1–325（325 aa）
Not recorded ZN ZINC ION × 4 MG MAGNESIUM ION × 4 RLT N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7PEL CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma Deposited 2021-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–325（325 aa）
Chain F 1–325（325 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
7Z1Z MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution Deposited 2022-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric
Chain Q 347–435（89 aa）
Chain R 347–435（89 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5；310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–530（530 aa）
Chain L 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–530（530 aa）
Chain L 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain K 1–530（530 aa）
Chain L 1–530（530 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9BW9 Tetrameric Complex of full-length HIV-1 integrase protein bound to the integrase binding domain of LEDGF/p75 Deposited 2024-05-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 347–435（89 aa）
Chain F 347–435（89 aa）
Chain G 347–435（89 aa）
Chain H 347–435（89 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C
Resolution 4.10 Å
9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain l 2–530（529 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

34 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PSIP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–105； UniProt 3–100

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3zeh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zeh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zeh
Deposition date deposition_date2012-12-05
Structure title titleSolution structure of the Hs. PSIP1 PWWP domain
Keywords keywordsDNA BINDING; DNA BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.62 Å
Radius of gyration Rg (electron density) rg_electron12.70 Å
Forward intensity I(0) i0560663000.00
Molecular weight molecular_weight213450.0 kDa
Excluded volume excluded_volume271650 ų
Envelope volume envelope_volume23866 ų
Hydration-shell volume shell_volume13621 ų
Envelope diameter envelope_diameter48.5 Å
Shell Rg shell_rg20.73 Å
Envelope Rg envelope_rg15.14 Å
Shape Rg shape_rg12.64 Å
Total Rg total_rg13.09 Å
Total atoms total_atoms30120
Residues n_residues1860
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax47.2 Å
Rg (real space) rg_real12.57 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real5.6070e+08
I(0) uncertainty (real space) i0_real_error6.2160e+06
Rg (reciprocal space) rg_reciprocal12.57 Å
I(0) (reciprocal space) i0_reciprocal560700000.0000
Solution quality estimate total_estimate0.8031
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.5 Å
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.195
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha277500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.498; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3zeha1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.9 — Tudor/PWWP/MBT
Family Family familyb.34.9.2 — PWWP domain
Domain ID domain_idd3zeha2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3zehA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
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8. Citations (1)

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9. Files and Curves (10)