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2l3r

NMR structure of UHRF1 Tandem Tudor Domains in a complex with Histone H3 peptide

Method: SOLUTION NMR Dmax: 49.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase UHRF1

Homo sapiens

UniProt Q96T88

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 126–285 Fragment：unp residues 126-285 Histone H3 × 1 （Q3BDD9） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition：0.6 mM [U-100% 15N] protein, 0.6 mM [U-100% 13C] protein, 3 mM protein, 90% H2O/10% D2O | 90% H2O/10% D2O 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 2L3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2FAZ Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95 Deposited 2005-12-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UBIQUITIN-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Well Solution: 20.0% P3350, 0.2 M tri-Li Citrate; Protein Buffer: 20 mM Tris pH 8.0, 100 mM NaCl, 5 mM beta- mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.00 Å R-free 0.252
2FAZ Ubiquitin-Like Domain of Human Nuclear Zinc Finger Protein NP95 Deposited 2005-12-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UBIQUITIN-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Well Solution: 20.0% P3350, 0.2 M tri-Li Citrate; Protein Buffer: 20 mM Tris pH 8.0, 100 mM NaCl, 5 mM beta- mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.00 Å R-free 0.252
2LGG Structure of PHD domain of UHRF1 in complex with H3 peptide Deposited 2011-07-26 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–366（69 aa） Fragment：UNP RESIDUES 298-366
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGK NMR Structure of UHRF1 PHD domains in a complex with histone H3 peptide Deposited 2011-07-28 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–366（69 aa） Fragment：UNP RESIDUES 298-366
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7；293.13 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] entity_1-1, 1.8 mM entity_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGL NMR structure of the UHRF1 PHD domain Deposited 2011-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 298–366（69 aa） Fragment：PHD domain (UNP RESIDUES 298-366)
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7；293.15 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] entity_1-1, 137 mM sodium chloride-2, 10 mM potassium phosphate-3, 3 mM DTT-4, 2.7 mM potassium chloride-5, 0.1 mM sodium azide-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2PB7 Crystal Structure of the SRA domain of the human UHRF1 protein Deposited 2007-03-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 408–643（236 aa） Fragment：SRA domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；14-19% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.90 Å R-free 0.227
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–367（234 aa） Fragment：tandem Tudor domain, PHD finger (residues 134-366)
Mutation：residues 167-175 was deleted. ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 134–367（234 aa） Fragment：tandem Tudor domain, PHD finger (residues 134-366)
Mutation：residues 167-175 was deleted. ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 134–367（234 aa） Fragment：tandem Tudor domain, PHD finger (residues 134-366)
Mutation：residues 167-175 was deleted. ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 134–367（234 aa） Fragment：tandem Tudor domain, PHD finger (residues 134-366)
Mutation：residues 167-175 was deleted. No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASL Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：PHD finger domain
Not recorded ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10mM sodium citrate, 42% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.41 Å R-free 0.196
3BI7 Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF1 Deposited 2007-11-30 Different construct Different mutation/modification Different oligomeric state 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 414–617（204 aa） Fragment：SRA Domain: Residues 414-617
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 4 UNL UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well solution mixed in 1:1 ratio with a water solution containing 20% (w/v) Sucrose, 4% (w/v) Glucose, 18% (v/v) Glycerol and 18% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.197
3CLZ The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA Deposited 2008-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 414–617（204 aa） Fragment：SRA DOMAIN (UNP residues 414-617)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.231
3CLZ The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA Deposited 2008-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 414–617（204 aa） Fragment：SRA DOMAIN (UNP residues 414-617)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.231
3CLZ The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA Deposited 2008-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 414–617（204 aa） Fragment：SRA DOMAIN (UNP residues 414-617)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.231
3CLZ The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA Deposited 2008-03-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 414–617（204 aa） Fragment：SRA DOMAIN (UNP residues 414-617)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12 % PEG 1500, 0.1 M BIS-TRIS, 0.2 M NACL, 0.001 M TCEP, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.231
3DB3 Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide Deposited 2008-05-30 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–285（160 aa） Fragment：Tandem Tudor Domains (UNP residues 126-285)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.282
3DB4 Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 Deposited 2008-05-30 Different construct Different mutation/modification Different oligomeric state 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 126–285（160 aa） Fragment：Tandem Tudor Domains (UNP residues 126-285)
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；10 % PEG 8000, 0.1 M SODIUM CACODYLATE, 0.2 M AMMONIUM SULFATE, 0.001 M TCEP, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.285
3DWH Structural and Functional Analysis of SRA domain Deposited 2008-07-22 Different construct Different oligomeric state 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 414–617（204 aa） Fragment：SRA domain, YDG Domain, residues 414-617
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；100mM Tris-Hcl 1.2M ammonium Sulfate 0.2M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.253
3FL2 Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1 Deposited 2008-12-18 Different construct Different oligomeric state 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 672–793（122 aa） Fragment：ring domain (UNP residues 672-793)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；27% PEG MME 2000, 0.1 M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.250
3SHB Crystal Structure of PHD Domain of UHRF1 Deposited 2011-06-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–366（69 aa） Fragment：PHD domain (UNP RESIDUES 298-366)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TRIS hydrochloride (pH8.5), 30% w/v Polyethylene glycerol 4000, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.228
3SOU Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide Deposited 2011-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.80 Å R-free 0.243
3SOU Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide Deposited 2011-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.80 Å R-free 0.243
3SOU Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide Deposited 2011-06-30 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 × 4 PDB declaration: tetrameric
Chain A 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.80 Å R-free 0.243
3SOW Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide Deposited 2011-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.95 Å R-free 0.247
3SOW Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide Deposited 2011-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.95 Å R-free 0.247
3SOW Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide Deposited 2011-06-30 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 × 4 PDB declaration: tetrameric
Chain A 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% w/v polyethylene glycol 8,000, 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.95 Å R-free 0.247
3SOX Structure of UHRF1 PHD finger in the free form Deposited 2011-06-30 Different construct Different oligomeric state 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 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.294
3SOX Structure of UHRF1 PHD finger in the free form Deposited 2011-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.294
3SOX Structure of UHRF1 PHD finger in the free form Deposited 2011-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.294
3SOX Structure of UHRF1 PHD finger in the free form Deposited 2011-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 298–367（70 aa） Fragment：UHRF1 (UNP Residues 298-367)
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.294
3T6R Structure of UHRF1 in complex with unmodified H3 N-terminal tail Deposited 2011-07-29 Different construct Different oligomeric state 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 299–364（66 aa） Fragment：UNP residues 299-364
Not recorded ZN ZINC ION × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M MgCl2, 0.1M Tris-HCl, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å R-free 0.229
3T6R Structure of UHRF1 in complex with unmodified H3 N-terminal tail Deposited 2011-07-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 299–364（66 aa） Fragment：UNP residues 299-364
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2M MgCl2, 0.1M Tris-HCl, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å R-free 0.229
3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 296–367（72 aa） Fragment：PHD FINGER, RESIDUES 296-367
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
Resolution 1.95 Å R-free 0.227
3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 296–367（72 aa） Fragment：PHD FINGER, RESIDUES 296-367
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
Resolution 1.95 Å R-free 0.227
3ZVZ PHD finger of human UHRF1 Deposited 2011-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 314–367（54 aa） Fragment：PHD FINGER, RESIDUES 314-367
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.45 Å R-free 0.197
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–366（233 aa） Fragment：Tudor PHD domain, UNP residues 134-366
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 134–366（233 aa） Fragment：Tudor PHD domain, UNP residues 134-366
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 134–366（233 aa） Fragment：Tudor PHD domain, UNP residues 134-366
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 134–366（233 aa） Fragment：Tudor PHD domain, UNP residues 134-366
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4QQD Crystal Structure of tandem tudor domains of UHRF1 in complex with a small organic molecule Deposited 2014-06-27 Different oligomeric state 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 126–285（160 aa） Fragment：unp residues 126-285
Not recorded 36X 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine × 2 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；20% PEG-3350, 0.2 M magnesium nitrate, vapor diffusion, sitting drop
Resolution 2.28 Å R-free 0.250
4QQD Crystal Structure of tandem tudor domains of UHRF1 in complex with a small organic molecule Deposited 2014-06-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 126–285（160 aa） Fragment：unp residues 126-285
Not recorded 36X 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine × 1 UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；20% PEG-3350, 0.2 M magnesium nitrate, vapor diffusion, sitting drop
Resolution 2.28 Å R-free 0.250
5C6D Crystal structure of USP7 in complex with UHRF1 Deposited 2015-06-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 634–665（32 aa） Fragment：UNP residues 634-665
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；100 mM CHES (pH 9.0), 20% PEG8000
Resolution 2.29 Å R-free 0.234
5C6D Crystal structure of USP7 in complex with UHRF1 Deposited 2015-06-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 634–665（32 aa） Fragment：UNP residues 634-665
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；100 mM CHES (pH 9.0), 20% PEG8000
Resolution 2.29 Å R-free 0.234
5IAY NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide Deposited 2016-02-22 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–285（152 aa） Fragment：UNP residues 134-285
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；297.15 K
NMR sample composition 1.0 mM [U-13C; U-15N] TTD, 1.2 mM Spacer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-15N] Spacer, TTD, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XPI Structure of UHRF1 TTD in complex with NV01 Deposited 2017-06-02 Different construct Different oligomeric state 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 127–283（157 aa） Fragment：UNP residues 127-283
Not recorded 8C3 N-[3-(diethylamino)propyl]-2-(12-methyl-9-oxidanylidene-5-thia-1,10,11-triazatricyclo[6.4.0.0^2,6]dodeca-2(6),3,7,11-tetraen-10-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；293 K；2.7 M Na formate and 0.1 M Na acetate pH 5.2
Resolution 2.20 Å R-free 0.219
5YY9 Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3 Deposited 2017-12-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 123–285（163 aa） Fragment：Tandem Tudor Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；00 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG 3350
Resolution 2.65 Å R-free 0.288
5YY9 Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3 Deposited 2017-12-08 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 123–285（163 aa） Fragment：Tandem Tudor Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；00 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG 3350
Resolution 2.65 Å R-free 0.288
5YYA Crystal structure of Tandem Tudor Domain of human UHRF1 Deposited 2017-12-08 Different construct Different oligomeric state 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 123–285（163 aa） Fragment：Tandem Tudor Domain
Not recorded EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M Bis-Tris (pH 6.5), 200 mM ammonium acetate, 25% (w/v) polyethylene glycol (PEG) 3350
Resolution 1.70 Å R-free 0.205
6B9M Crystal structure of UHRF1 TTD domain in complex with the polybasic region Deposited 2017-10-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 638–678（41 aa） Fragment：unp residues 638-678
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Succinic acid pH7.0, 15% (v/v) Polyethylene glycol 3350
Resolution 1.68 Å R-free 0.207
6IIW Crystal structure of human UHRF1 PHD finger in complex with PAF15 Deposited 2018-10-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 299–366（68 aa）
Not recorded ZN ZINC ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES (pH 7.5), 70% (v/v) MPD
Resolution 1.70 Å R-free 0.189
6VCS SRA domain of UHRF1 in complex with DNA Deposited 2019-12-22 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 × 4 PDB declaration: hexameric
Chain A 427–630（204 aa）
Chain B 427–630（204 aa）
Chain E 427–630（204 aa）
Not recorded UNX UNKNOWN LIGAND × 66 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M sodium malonate, 12% PEG3350
Resolution 1.70 Å R-free 0.258
6VED Solution structure of the TTD and linker region of UHRF1 Deposited 2019-12-31 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 146–313（168 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 250 uM [U-99% 13C; U-99% 15N] TTD-linker, 150 mM sodium chloride, 25 mM sodium phosphate, 5 mM DTT, 2 mM beta-mercaptoethanol, 2 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6VYJ Human UHRF1 TTD domain in complex with a fragment Deposited 2020-02-26 Different construct Different oligomeric state 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 122–283（162 aa）
Not recorded RVV 2,4-dimethylpyridine × 2 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50 mM Bis-Tris, pH 5.75, 35 % w/v PEG 3350. The crystals were cryo-preserved by 25% glucose
Resolution 1.39 Å R-free 0.226
6W92 Human UHRF1 TTD domain Deposited 2020-03-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 135–296（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；295 K；0.1 M Bis-Tris, pH = 5.5, 25 % w/v PEG 3350
Resolution 1.30 Å R-free 0.185
7FB7 Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine Deposited 2021-07-08 Different construct Different oligomeric state 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 123–285（163 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 8NF 5-amino-2,4-dimethylpyridine × 1 DMS DIMETHYL SULFOXIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES (pH7.5), 45% v/v MPD, 0.2 M Ammonium acetate
Resolution 1.45 Å R-free 0.173
7FB7 Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine Deposited 2021-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 123–285（163 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 8NF 5-amino-2,4-dimethylpyridine × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES (pH7.5), 45% v/v MPD, 0.2 M Ammonium acetate
Resolution 1.45 Å R-free 0.173
8JIG A Novel UHRF1-Targeted Compound Deposited 2023-05-26 Different construct Different oligomeric state 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 414–617（204 aa）
Not recorded 8JA N-[2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-N'-oxidanyl-octanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bris-Tris, pH 6.0, 0.2M NaCl, 1mM TCEP, 2.2-2.4mM ammonium sulfate
Resolution 2.40 Å R-free 0.244
8JIG A Novel UHRF1-Targeted Compound Deposited 2023-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 414–617（204 aa）
Not recorded 8JA N-[2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-N'-oxidanyl-octanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bris-Tris, pH 6.0, 0.2M NaCl, 1mM TCEP, 2.2-2.4mM ammonium sulfate
Resolution 2.40 Å R-free 0.244
8WMS Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain Deposited 2023-10-04 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 299–366（68 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG3,350
Resolution 2.40 Å R-free 0.266
8XV4 Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.6 M NaCl, 0.1 M MES pH6.5, 20% PEG4000
Resolution 3.20 Å R-free 0.266
8XV4 Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.6 M NaCl, 0.1 M MES pH6.5, 20% PEG4000
Resolution 3.20 Å R-free 0.266
8XV6 Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：PHD domain
Not recorded SCN THIOCYANATE ION × 3 GOL GLYCEROL × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Potassium thiocyanate, 30% PEG MME2000
Resolution 1.60 Å R-free 0.168
8XV6 Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 298–367（70 aa） Fragment：PHD domain
Not recorded SCN THIOCYANATE ION × 3 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Potassium thiocyanate, 30% PEG MME2000
Resolution 1.60 Å R-free 0.168
8XV7 Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 3 GOL GLYCEROL × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4% v/v Tacsimate pH 7.0, 12% PEG 3350
Resolution 2.25 Å R-free 0.226
8XV7 Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4% v/v Tacsimate pH 7.0, 12% PEG 3350
Resolution 2.25 Å R-free 0.226
8XV7 Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4% v/v Tacsimate pH 7.0, 12% PEG 3350
Resolution 2.25 Å R-free 0.226
8XV7 Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 134–366（233 aa） Fragment：TTD-PHD domain
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；4% v/v Tacsimate pH 7.0, 12% PEG 3350
Resolution 2.25 Å R-free 0.226
8XV8 Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 298–367（70 aa） Fragment：PHD domain
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
Resolution 2.05 Å R-free 0.207
8XV8 Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 298–367（70 aa） Fragment：PHD domain
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
Resolution 2.05 Å R-free 0.207
8XV8 Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 298–367（70 aa） Fragment：PHD domain
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
Resolution 2.05 Å R-free 0.207
8XV8 Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121) Deposited 2024-01-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 298–367（70 aa） Fragment：PHD domain
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350
Resolution 2.05 Å R-free 0.207
9LN6 Structure of human NLRP14-UHRF1 complex Deposited 2025-01-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–78（78 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
9LPK Structure of human PADI6-UHRF1-UBE2D3 complex Deposited 2025-01-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–793（793 aa）
Chain F 1–793（793 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.03 Å
9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–793（793 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–793（793 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

44 other PDB entries and 76 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UHRF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–162； UniProt 126–285

Histone H3

OrganismNot specified

UniProt Q3BDD9

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2–12 Non-standard monomer：Yes (specific site not provided by mmCIF) E3 ubiquitin-protein ligase UHRF1 × 1 （Q96T88） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1 NMR sample composition：0.6 mM [U-100% 15N] protein, 0.6 mM [U-100% 13C] protein, 3 mM protein, 90% H2O/10% D2O | 90% H2O/10% D2O 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 2L3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FDT Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide Deposited 2008-11-26 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；35% PEG 400, 0.2M Na Cl, 0.1M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.257

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q3BDD9_9INSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–11； UniProt 2–12

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 2l3r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l3r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l3r
Deposition date deposition_date2010-09-21
Structure title titleNMR structure of UHRF1 Tandem Tudor Domains in a complex with Histone H3 peptide
Keywords keywords;tudor domain, heterochromatin, transcriptional repression, Structural Genomics, Structural Genomics Consortium, SGC, DNA BINDING PROTEIN, DNA BINDING PROTEIN-GENE REGULATION complex ;; DNA BINDING PROTEIN/GENE REGULATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.15 Å
Radius of gyration Rg (electron density) rg_electron17.90 Å
Forward intensity I(0) i01380260000.00
Molecular weight molecular_weight301300.0 kDa
Excluded volume excluded_volume371510 ų
Envelope volume envelope_volume44609 ų
Hydration-shell volume shell_volume19245 ų
Envelope diameter envelope_diameter82.8 Å
Shell Rg shell_rg26.52 Å
Envelope Rg envelope_rg21.28 Å
Shape Rg shape_rg17.83 Å
Total Rg total_rg18.27 Å
Total atoms total_atoms41775
Residues n_residues2565
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 dmax49.5 Å
Rg (real space) rg_real17.00 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real1.3140e+09
I(0) uncertainty (real space) i0_real_error1.2340e+07
Rg (reciprocal space) rg_reciprocal18.34 Å
I(0) (reciprocal space) i0_reciprocal1380000000.0000
Solution quality estimate total_estimate0.6801
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.380
Kurtosis Kurtosis kurtosis-0.260
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha2.6770
Highest regularization parameter α highest_alpha1698000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.957; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2l3rA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily140 —
Domain ID domain_id2l3rA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30 —
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8. Citations (1)

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9. Files and Curves (10)