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- PDB-4wxx: The crystal structure of human DNMT1(351-1600) -

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Basic information

Entry
Database: PDB / ID: 4wxx
TitleThe crystal structure of human DNMT1(351-1600)
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / DNMT1 / DNA methytransferase1 / DNA methylation
Function / homology
Function and homology information


negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins ...negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / negative regulation of gene expression via chromosomal CpG island methylation / female germ cell nucleus / methyl-CpG binding / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / DNA methylation / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / NoRC negatively regulates rRNA expression / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site ...DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.622 Å
AuthorsZhang, Z.M. / Song, J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Crystal Structure of Human DNA Methyltransferase 1.
Authors: Zhang, Z.M. / Liu, S. / Lin, K. / Luo, Y. / Perry, J.J. / Wang, Y. / Song, J.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Structure summary
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
B: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,62714
Polymers284,2042
Non-polymers1,42312
Water11,476637
1
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8137
Polymers142,1021
Non-polymers7116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8137
Polymers142,1021
Non-polymers7116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.568, 138.568, 221.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / CXXC-type zinc finger protein 9 / DNA methyltransferase HsaI / MCMT


Mass: 142102.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1, AIM, CXXC9, DNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 45% PEG200, 50 mM CaCl2, 0.1 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.62→48.22 Å / Num. obs: 122755 / % possible obs: 98.6 % / Redundancy: 5.2 % / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.622→48.215 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 6102 4.97 %
Rwork0.2049 --
obs0.2069 122708 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.622→48.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18336 0 62 637 19035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318840
X-RAY DIFFRACTIONf_angle_d0.79225518
X-RAY DIFFRACTIONf_dihedral_angle_d14.4527000
X-RAY DIFFRACTIONf_chiral_restr0.032735
X-RAY DIFFRACTIONf_plane_restr0.0043339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6222-2.6520.36692110.30623656X-RAY DIFFRACTION93
2.652-2.68320.30462280.26823878X-RAY DIFFRACTION99
2.6832-2.71590.28842150.26663921X-RAY DIFFRACTION99
2.7159-2.75030.30282100.25293866X-RAY DIFFRACTION99
2.7503-2.78650.28891750.2513937X-RAY DIFFRACTION99
2.7865-2.82460.28161990.24473892X-RAY DIFFRACTION99
2.8246-2.8650.34142190.24373908X-RAY DIFFRACTION99
2.865-2.90770.26692310.23453886X-RAY DIFFRACTION99
2.9077-2.95320.29741620.24283963X-RAY DIFFRACTION99
2.9532-3.00160.28732410.23663871X-RAY DIFFRACTION99
3.0016-3.05330.31112210.23153870X-RAY DIFFRACTION99
3.0533-3.10880.25322050.23553917X-RAY DIFFRACTION99
3.1088-3.16860.27162000.22853885X-RAY DIFFRACTION99
3.1686-3.23330.29531790.23573941X-RAY DIFFRACTION99
3.2333-3.30360.29121860.24823897X-RAY DIFFRACTION99
3.3036-3.38040.26512140.22373931X-RAY DIFFRACTION99
3.3804-3.46490.28662190.21713875X-RAY DIFFRACTION99
3.4649-3.55860.25912180.21273900X-RAY DIFFRACTION99
3.5586-3.66330.23262130.20593838X-RAY DIFFRACTION99
3.6633-3.78150.24491710.19813944X-RAY DIFFRACTION99
3.7815-3.91650.24162220.19713859X-RAY DIFFRACTION99
3.9165-4.07330.25111900.18993912X-RAY DIFFRACTION99
4.0733-4.25860.23471970.17813871X-RAY DIFFRACTION98
4.2586-4.48290.18381850.16813929X-RAY DIFFRACTION98
4.4829-4.76360.18432180.16323879X-RAY DIFFRACTION98
4.7636-5.1310.20512210.17573862X-RAY DIFFRACTION98
5.131-5.64660.2251870.19363884X-RAY DIFFRACTION98
5.6466-6.4620.22662160.19883865X-RAY DIFFRACTION98
6.462-8.13510.22321630.18733917X-RAY DIFFRACTION97
8.1351-48.22280.19461860.1753852X-RAY DIFFRACTION96

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