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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 126–285 | Fragment：unp residues 126-285 | 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 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 126–285 | Fragment：unp residues 126-285 | 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 |
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 4QQD | 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 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 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 |
| 3SHB Crystal Structure of PHD Domain of UHRF1 Deposited 2011-06-16 | Different construct Different oligomeric state Different ligand/ion 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 oligomeric state 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：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 oligomeric state Different ligand/ion 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 oligomeric state 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：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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 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 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 |
| 5C6D Crystal structure of USP7 in complex with UHRF1 Deposited 2015-06-22 | Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 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 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 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 oligomeric state 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 |
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 oligomeric state 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 × 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 | 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 oligomeric state 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 | 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 oligomeric state 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 oligomeric state 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 75 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 2–161； UniProt 126–285 Author chain B； PDBConstruct 2–161； UniProt 126–285 |