3shb

Crystal Structure of PHD Domain of UHRF1

Method: X-RAY DIFFRACTION D_max: 44.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase UHRF1

Homo sapiens

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 298–366	Fragment：PHD domain (UNP RESIDUES 298-366)	Histone H3 peptide × 1 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

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 3SHB	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 ligand/ion 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 ligand/ion 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
2L3R NMR structure of UHRF1 Tandem Tudor Domains in a complex with Histone H3 peptide Deposited 2010-09-21	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 126–285（160 aa） Fragment：unp residues 126-285	Not recorded	No recorded non-water small molecule	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
2LGG Structure of PHD domain of UHRF1 in complex with H3 peptide Deposited 2011-07-26	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：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 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：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 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 298–366（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 ligand/ion 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 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 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 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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
3SOU Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide Deposited 2011-06-30	Different construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 construct Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–285（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 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 9–77； UniProt 298–366

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3shb
Deposition date deposition_date	2011-06-16
Structure title title	Crystal Structure of PHD Domain of UHRF1
Keywords keywords	unmodified Histone, methylation, UHRF1, PHD, H3, LIGASE-NUCLEAR PROTEIN complex; LIGASE/NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.07 Å
Radius of gyration Rg (electron density) rg_electron	12.15 Å
Forward intensity I(0) i0	2092740.00
Molecular weight molecular_weight	8610.0 kDa
Excluded volume excluded_volume	10131 Å³
Envelope volume envelope_volume	11720 Å³
Hydration-shell volume shell_volume	8579 Å³
Envelope diameter envelope_diameter	42.2 Å
Shell Rg shell_rg	17.32 Å
Envelope Rg envelope_rg	12.77 Å
Shape Rg shape_rg	12.22 Å
Total Rg total_rg	13.14 Å
Total atoms total_atoms	578
Residues n_residues	74
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	44.4 Å
Rg (real space) rg_real	13.06 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.0930e+06
I(0) uncertainty (real space) i0_real_error	2.6530e+04
Rg (reciprocal space) rg_reciprocal	13.06 Å
I(0) (reciprocal space) i0_reciprocal	2093000.0000
Solution quality estimate total_estimate	0.8615
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.3 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.120
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	163600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase UHRF1
Molecular weight formula_weight	8634.8 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	644

GPLGSPEFSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H3 peptide
Molecular weight formula_weight	1308.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ARTKQTARKSTG

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3shbA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	36.609 Å
Unit-cell length b length_b	36.609 Å
Unit-cell length c length_c	219.765 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	31.704 Å
R factor r_factor	0.2107
R_work r_work	0.2099
R_free r_free	0.2278

fit	/app/data/saxs_computation/sh/3shb/3shb.fit
pddf	/app/data/pr_computation/sh/3shb/3shb.pr.out
profile	/app/data/saxs_computation/sh/3shb/3shb.dat

Crystal Structure of PHD Domain of UHRF1

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase UHRF1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)