SAXSdb — 8xqc

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

DNA (cytosine-5)-methyltransferase 1

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 351–1616	Not recorded	;DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') ; × 1 ;DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') ; × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.25 Å

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 8XQC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EPZ Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 Deposited 2008-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 351–600（250 aa） Fragment：REPLICATION FOCI-TARGETING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 BGC beta-D-glucopyranose × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；23 % PEG 3350, 0.1 M BIS-TRIS PH 6.0,0.2 M SODIUM ACETATE, 0.005 M TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 6.00	Resolution 2.31 Å R-free 0.264
3EPZ Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 Deposited 2008-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 351–600（250 aa） Fragment：REPLICATION FOCI-TARGETING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；23 % PEG 3350, 0.1 M BIS-TRIS PH 6.0,0.2 M SODIUM ACETATE, 0.005 M TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 6.00	Resolution 2.31 Å R-free 0.264
3PTA Crystal structure of human DNMT1(646-1600) in complex with DNA Deposited 2010-12-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 646–1600（955 aa） Fragment：UNP residues 646-1600	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；6% PEG 20,000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.60 Å R-free 0.291
3SWR Structure of human DNMT1 (601-1600) in complex with Sinefungin Deposited 2011-07-14	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 601–1600（1000 aa） Fragment：sequence database residues 601-1600	Not recorded	SFG SINEFUNGIN × 1 SO4 SULFATE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 25 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；289 K；5% PEG 4000, 5 mM MgSO4, 50 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.272
4WXX The crystal structure of human DNMT1(351-1600) Deposited 2014-11-14	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 15–1264（1250 aa）	Not recorded	ZN ZINC ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；45% PEG200, 50 mM CaCl2, 0.1 mM MES	Resolution 2.62 Å R-free 0.245
4WXX The crystal structure of human DNMT1(351-1600) Deposited 2014-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 15–1264（1250 aa）	Not recorded	ZN ZINC ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；45% PEG200, 50 mM CaCl2, 0.1 mM MES	Resolution 2.62 Å R-free 0.245
4YOC Crystal Structure of human DNMT1 and USP7/HAUSP complex Deposited 2015-03-11	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 600–1600（1001 aa） Fragment：UNP RESIDUES 600-1600	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；6-8% PEG 3350, 200 mM potassium acetate	Resolution 2.92 Å R-free 0.258
4Z96 Crystal structure of DNMT1 in complex with USP7 Deposited 2015-04-09	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 C 1097–1129（33 aa） Fragment：UNP residues 1097-1129	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH5.5, 10% PEG6000, 15% glycerol	Resolution 2.85 Å R-free 0.246
5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 351–600（250 aa） Fragment：RFTS domain, UNP residues 351-600	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000	Resolution 2.00 Å R-free 0.239
5YDR Structure of DNMT1 RFTS domain in complex with ubiquitin Deposited 2017-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 351–599（249 aa） Fragment：RFTS domain, UNP residues 351-599	Not recorded	PO4 PHOSPHATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8；291 K；20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000	Resolution 2.00 Å R-free 0.233
6L1F Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1 Deposited 2019-09-29	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 × 2 PDB declaration: dimeric	Chain A 140–145（6 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG MME 2000, 0.1M sodium cacodylate, pH 6.0	Resolution 1.90 Å R-free 0.230
6X9I Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA Deposited 2020-06-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.20 Å R-free 0.225
6X9J Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 Deposited 2020-06-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 X52 N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 1.79 Å R-free 0.229
6X9K Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A Deposited 2020-06-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 9 UXM (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.65 Å R-free 0.228
7SFC Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A Deposited 2021-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	ZN ZINC ION × 2 I67 N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide × 3 EDO 1,2-ETHANEDIOL × 19 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 1.97 Å R-free 0.208
7SFD Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A Deposited 2021-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 IO5 (2S)-2-({3,5-dicyano-4-ethyl-6-[4-(2-hydroxyethyl)-1,4-diazepan-1-yl]pyridin-2-yl}sulfanyl)-2-phenylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.09 Å R-free 0.216
7SFE Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A Deposited 2021-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 ZN ZINC ION × 2 GOL GLYCEROL × 1 96I (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.55 Å R-free 0.236
7SFF Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B Deposited 2021-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 C79 (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.05 Å R-free 0.217
7SFG Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM Deposited 2021-10-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 393–1264（872 aa）	Not recorded	ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)	Resolution 2.43 Å R-free 0.223
7XI9 Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form) Deposited 2022-04-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 351–1616（1266 aa）	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging	Resolution 2.52 Å
7XIB Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form) Deposited 2022-04-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 351–1616（1266 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging	Resolution 2.23 Å
8V9U Solution NMR structure of human DNMT1 N-terminal alpha-helical domain Deposited 2023-12-09	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 16–93（78 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 1 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 5 % pentaethylene glycol monododecyl ether (C12E5), 95 % n-hexanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9K2W Cryo-EM structure of USP7:DNMT1 complex; closed conformation Deposited 2024-10-18	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 351–1616（1266 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
9K2X Cryo-EM structure of USP7:DNMT1 complex; open conformation Deposited 2024-10-18	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 351–1616（1266 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
9V36 Human DNMT1 (aa 698-1616) bound to hemimethylated dsDNA and Inhibitor DMI26 Deposited 2025-05-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 698–1616（919 aa）	Not recorded	ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 A1EQT (2~{R})-2-[3,5-dicyano-1-[2-[2-(dimethylamino)ethyl-methyl-amino]-2-oxidanylidene-ethyl]-4-ethyl-pyrrolo[2,3-b]pyridin-6-yl]sulfanyl-2-phenyl-ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
9V5P Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207 Deposited 2025-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 698–1616（919 aa）	Not recorded	ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 A1EQ2 (2~{R})-2-[3,5-dicyano-1-[2-[2-(dimethylamino)ethyl-methyl-amino]-2-oxidanylidene-ethyl]-4-ethyl-pyrrolo[2,3-b]pyridin-6-yl]sulfanyl-2-(4-methoxyphenyl)ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å

24 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–1271； UniProt 351–1616

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	8xqc
Deposition date deposition_date	2024-01-05
Structure title title	Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog
Keywords keywords	DNA methyltransferase, protein-DNA complex, replication factor, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	31.68 Å
Radius of gyration Rg (electron density) rg_electron	31.07 Å
Forward intensity I(0) i0	186736000.00
Molecular weight molecular_weight	103300.0 kDa
Excluded volume excluded_volume	126800 Å³
Envelope volume envelope_volume	164650 Å³
Hydration-shell volume shell_volume	43723 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	38.36 Å
Envelope Rg envelope_rg	31.29 Å
Shape Rg shape_rg	31.07 Å
Total Rg total_rg	31.67 Å
Total atoms total_atoms	7233
Residues n_residues	864
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	103.0 Å
Rg (real space) rg_real	31.60 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.8670e+08
I(0) uncertainty (real space) i0_real_error	2.8570e+06
Rg (reciprocal space) rg_reciprocal	31.64 Å
I(0) (reciprocal space) i0_reciprocal	186700000.0000
Solution quality estimate total_estimate	0.8998
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	43440000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA (cytosine-5)-methyltransferase 1
Molecular weight formula_weight	143559.5 kDa
EC 编号 ec_number	2.1.1.37
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	7233

GPPTTPKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCFSVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARRQTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMAMKEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKARESASAKIKEEEAAKD

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') ;
Molecular weight formula_weight	3725.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACTTACGGAAGG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPCPTPTPCP(C55)PGPTPAPAPGPT)-3') ;
Molecular weight formula_weight	3679.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CCTTCCGTAAGT

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.25 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	356895

fit	/app/data/saxs_computation/xq/8xqc/8xqc.fit
pddf	/app/data/pr_computation/xq/8xqc/8xqc.pr.out
profile	/app/data/saxs_computation/xq/8xqc/8xqc.dat

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

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

DNA (cytosine-5)-methyltransferase 1

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)