SAXSdb — 3f8i

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

E3 ubiquitin-protein ligase UHRF1

Mus musculus

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 418–628	Fragment：YDG domain: UNP residues 419-628	5'-D(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3' × 1 5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277 K；20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.29 Å R-free 0.268
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 418–628	Fragment：YDG domain: UNP residues 419-628	5'-D(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3' × 1 5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；277 K；20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.29 Å R-free 0.268

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 3F8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
12DL Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs Deposited 2026-03-29	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 × 33 PDB declaration: 33-meric	Chain BA 1–782（782 aa） Chain BB 1–782（782 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 11 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
24MC Structure of oocyte cytoplasmic lattices Deposited 2026-03-10	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 × 36 PDB declaration: 36-meric	Chain b 1–782（782 aa） Chain d 1–782（782 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
2ZKD Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA Deposited 2008-03-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate (pH5.6), 0.2M sodium acetate, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.185
2ZKD Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA Deposited 2008-03-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate (pH5.6), 0.2M sodium acetate, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.185
2ZKE Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA Deposited 2008-03-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M Bis-Tris-propane (pH7.5), 0.2M sodium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.275
2ZKF Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA Deposited 2008-03-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M Bis-Tris-propane (pH7.5), 0.2M sodium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.275
2ZKG Crystal structure of unliganded SRA domain of mouse Np95 Deposited 2008-03-19	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 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.77 Å R-free 0.217
2ZKG Crystal structure of unliganded SRA domain of mouse Np95 Deposited 2008-03-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.77 Å R-free 0.217
2ZKG Crystal structure of unliganded SRA domain of mouse Np95 Deposited 2008-03-19	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 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.77 Å R-free 0.217
2ZKG Crystal structure of unliganded SRA domain of mouse Np95 Deposited 2008-03-19	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 404–613（210 aa） Fragment：UNP residues 404-613	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.77 Å R-free 0.217
2ZO0 mouse NP95 SRA domain DNA specific complex 1 Deposited 2008-05-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；20% (v/v) polyethylene glycol 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.19 Å R-free 0.253
2ZO0 mouse NP95 SRA domain DNA specific complex 1 Deposited 2008-05-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；20% (v/v) polyethylene glycol 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.19 Å R-free 0.253
2ZO1 Mouse NP95 SRA domain DNA specific complex 2 Deposited 2008-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；20% (v/v) polyethylene glycol 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.96 Å R-free 0.246
2ZO1 Mouse NP95 SRA domain DNA specific complex 2 Deposited 2008-05-05	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 B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；20% (v/v) polyethylene glycol 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.96 Å R-free 0.246
2ZO2 Mouse NP95 SRA domain non-specific DNA complex Deposited 2008-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；20% (v/v) polyethylene glycol 3350 or 10000, 0.2-0.4M NaCl, 0.1M MES(pH 5.8-6.2), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.09 Å R-free 0.291
2ZO2 Mouse NP95 SRA domain non-specific DNA complex Deposited 2008-05-05	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 B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；20% (v/v) polyethylene glycol 3350 or 10000, 0.2-0.4M NaCl, 0.1M MES(pH 5.8-6.2), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.09 Å R-free 0.291
2ZO2 Mouse NP95 SRA domain non-specific DNA complex Deposited 2008-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain B 419–628（210 aa） Fragment：SRA domain, residues 419-628	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；20% (v/v) polyethylene glycol 3350 or 10000, 0.2-0.4M NaCl, 0.1M MES(pH 5.8-6.2), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.09 Å R-free 0.291
3F8J Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group C222(1) Deposited 2008-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 417–628（212 aa） Fragment：YDG domain: UNP residues 417-628	Not recorded	GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；277 K；20% PEG 3350, 0.4 M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 1.99 Å R-free 0.232
3FDE Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution Deposited 2008-11-25	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 419–628（210 aa） Fragment：YDG domain: UNP residues 419-628	Not recorded	EDO 1,2-ETHANEDIOL × 11 NA SODIUM ION × 2 UNL UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 1.41 Å R-free 0.186
3FDE Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution Deposited 2008-11-25	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 419–628（210 aa） Fragment：YDG domain: UNP residues 419-628	Not recorded	EDO 1,2-ETHANEDIOL × 11 NA SODIUM ION × 2 UNL UNKNOWN LIGAND × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；20% PEG 3350, 0.4M NaCl, pH 7.0, VAPOR DIFFUSION, temperature 277K	Resolution 1.41 Å R-free 0.186
6M2V Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. Deposited 2020-03-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 417–628（212 aa） Chain B 417–628（212 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1M Bis-Tris, pH 8.0, 0.2M NaCl, 12% PEG 3,350	Resolution 3.00 Å R-free 0.276
6VEE Solution structure of the TTD and linker region of mouse UHRF1 (NP95) Deposited 2019-12-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–305（184 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, 50 mM sodium phosphate, 5 mM DTT, 5 mM TCEP, 2 mM beta-mercaptoethanol, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6VFO Solution structure of the PHD of mouse UHRF1 (NP95) Deposited 2020-01-06	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 303–380（78 aa）	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 7.5；290 K；Ionic strength (raw mmCIF value) 150；Pressure 1 NMR sample composition 200 uM [U-99% 13C; U-99% 15N] PHD, 5 mM DTT, 2 mM beta-mercaptoethanol, 5 mM TCEP, 150 mM sodium chloride, 50 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7XGA NMR strucutre of chimeric protein for model of PHD-Stella complex Deposited 2022-04-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 304–372（69 aa）	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.66 mM [U-100% 13C; U-100% 15N] PHD_Stella, 10 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.66 mM [U-100% 13C; U-100% 15N] PHD_Stella, 10 mM sodium phosphate, 50 mM sodium chloride, 100% D2O \| 100% D2O	Resolution not provided
9SFP Native cytoplasmic lattices from mouse oocytes Deposited 2025-08-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric	Chain d 1–782（782 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
9W2M Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte Deposited 2025-07-28	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 × 56 PDB declaration: 56-meric	Chain P 1–782（782 aa） Chain Q 1–782（782 aa） Chain p 1–782（782 aa） Chain q 1–782（782 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9XRL Structure of mouse cytoplasmic lattice (CPL) repeating unit Deposited 2025-11-19	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 × 73 PDB declaration: 73-meric	Chain AL 1–782（782 aa） Chain AR 1–782（782 aa） Chain x 1–782（782 aa）	Not recorded	ZN ZINC ION × 13 GTP GUANOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

18 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UHRF1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–212； UniProt 418–628 Author chain B； PDBConstruct 2–212； UniProt 418–628

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3f8i
Deposition date deposition_date	2008-11-12
Structure title title	Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21
Keywords keywords	;UHRF1, base flipping, 5-methylcytosine, CpG methylation, Cell cycle, Developmental protein, DNA damage, DNA repair, DNA-binding, Ligase, Metal-binding, Nucleus, Phosphoprotein, Transcription, Transcription regulation, Ubl conjugation, Ubl conjugation pathway, Zinc, Zinc-finger, LIGASE-DNA COMPLEX ;; LIGASE/DNA
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	32.29 Å
Radius of gyration Rg (electron density) rg_electron	33.11 Å
Forward intensity I(0) i0	81881000.00
Molecular weight molecular_weight	59996.0 kDa
Excluded volume excluded_volume	69915 Å³
Envelope volume envelope_volume	99428 Å³
Hydration-shell volume shell_volume	26618 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	37.96 Å
Envelope Rg envelope_rg	31.98 Å
Shape Rg shape_rg	33.15 Å
Total Rg total_rg	33.35 Å
Total atoms total_atoms	4178
Residues n_residues	458
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	104.2 Å
Rg (real space) rg_real	32.60 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	8.1880e+07
I(0) uncertainty (real space) i0_real_error	1.3690e+06
Rg (reciprocal space) rg_reciprocal	32.48 Å
I(0) (reciprocal space) i0_reciprocal	81870000.0000
Solution quality estimate total_estimate	0.7981
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.382
Kurtosis Kurtosis kurtosis	-0.821
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10730000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.630; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.656; Smooth: 0.825

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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	23915.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4313

HMPANHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNYFTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVVRNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKDRTRQLGLTMQYPEGYLEALANKEKSRKR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(DCPDCPDAPDTPDGP(5CM)PDGPDCPDTPDGPDAPDC)-3'
Molecular weight formula_weight	3637.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,F

CCATGCGCTGAC

Entity 3 Entity 3 polymer

Description description	5'-D(DGPDTPDCPDAPDGPDCPDGPDCPDAPDTPDGPDG)-3'
Molecular weight formula_weight	3703.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GTCAGCGCATGG

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3f8ia1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

Domain ID domain_id	d3f8ia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3f8ib1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.12 — SRA domain-like

Domain ID domain_id	d3f8ib2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3f8iA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

Domain ID domain_id	3f8iB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	280 — PUA domain-like
Homologous superfamily homologous superfamily	10 — SRA-YDG

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8. Citations (2)

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Unit-cell length a length_a	50.084 Å
Unit-cell length b length_b	62.416 Å
Unit-cell length c length_c	113.447 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	34.530 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2680

fit	/app/data/saxs_computation/f8/3f8i/3f8i.fit
pddf	/app/data/pr_computation/f8/3f8i/3f8i.pr.out
profile	/app/data/saxs_computation/f8/3f8i/3f8i.dat

Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group P21

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 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)