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- PDB-3av5: Crystal structure of mouse DNA methyltransferase 1 with AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3av5
TitleCrystal structure of mouse DNA methyltransferase 1 with AdoHcy
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / CXXC-type zinc finger/C5-methyltransferase family / Methylates CpG residues / Preferentially methylates hemimethylated DNA / DNA binding / hemi-methylation / Nucleus
Function / homology
Function and homology information


SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / cellular response to bisphenol A ...SUMOylation of DNA methylation proteins / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / female germ cell nucleus / methyl-CpG binding / germ cell nucleus / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / heterochromatin / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / replication fork / methyltransferase activity / cellular response to amino acid stimulus / promoter-specific chromatin binding / regulation of cell population proliferation / regulation of gene expression / methylation / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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 (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. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsTakeshita, K. / Suetake, I. / Yamashita, E. / Suga, M. / Narita, H. / Nakagawa, A. / Tajima, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Authors: Takeshita, K. / Suetake, I. / Yamashita, E. / Suga, M. / Narita, H. / Nakagawa, A. / Tajima, S.
History
DepositionFeb 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,4436
Polymers150,7961
Non-polymers6465
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.993, 96.920, 130.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / Met-1 / DNA methyltransferase MmuI / DNA MTase MmuI / M.MmuI / MCMT


Mass: 150796.469 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-1620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Plasmid: pFastBacHTb / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.58 % / Mosaicity: 0.512 °
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 9
Details: PEG 3350, NaCl, TCEP, pH 9.0, vapor diffusion, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 10, 2010 / Details: mirror
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.25→200 Å / Num. obs: 26418 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.212 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.3-3.365.10.34412250.9397.8
3.36-3.425.20.29612310.90697.3
3.42-3.485.20.27212240.90796.5
3.48-3.555.20.23312460.96798
3.55-3.635.10.20112060.97197
3.63-3.725.20.16812510.97196.6
3.72-3.815.20.15512090.98696.7
3.81-3.915.20.13312260.98696.4
3.91-4.035.20.11912500.97996.5
4.03-4.165.20.10212070.98896.3
4.16-4.315.20.08812231.06696.5
4.31-4.485.20.07512311.10796.2
4.48-4.685.20.0712251.11696
4.68-4.935.20.07412341.26595.4
4.93-5.245.20.08612311.56495.7
5.24-5.645.10.09412331.9294.9
5.64-6.2150.09412412.01294.9
6.21-7.1150.08512352.15394.3
7.11-8.965.10.04512491.2293.6
8.96-2004.80.03212751.30189.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV4

3av4


Resolution: 3.25→38.66 Å / Cor.coef. Fo:Fc: 0.9108 / Cor.coef. Fo:Fc free: 0.8277 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 1367 5.17 %RANDOM
Rwork0.1835 ---
obs0.1876 26418 --
Displacement parametersBiso max: 166.59 Å2 / Biso mean: 59.65 Å2 / Biso min: 8.37 Å2
Baniso -1Baniso -2Baniso -3
1-10.5869 Å20 Å20 Å2
2---3.0858 Å20 Å2
3----7.5011 Å2
Refine analyzeLuzzati coordinate error obs: 0.536 Å
Refinement stepCycle: LAST / Resolution: 3.25→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9105 0 30 0 9135
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019353HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2512647HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3261SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes241HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1343HARMONIC5
X-RAY DIFFRACTIONt_it9353HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion23.94
X-RAY DIFFRACTIONt_improper_torsion1HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion1166SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10857SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.38 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3027 150 5.16 %
Rwork0.2016 2756 -
all0.207 2906 -
obs-2906 -
Refinement TLS params.

Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)
10.2650.15810.3110.41270.19790.40050.1561-0.32670.1092-0.0147-0.22160.37770.1751-0.35670.06550.0421-0.152-0.11360.196-0.06130.2146
21.26220.81250.45290.49420.32310.0916-0.0164-0.0283-0.00430.06270.02720.03410.07060.0463-0.0109-0.01380.0118-0.02060.0168-0.0115-0.0031
30.16681.11270.39860.59910.51770.29440.00440.00480.00230.10180.01580.0523-0.0515-0.01-0.02020.0193-0.0138-0.021-0.0033-0.0107-0.0163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }0
2X-RAY DIFFRACTION2{ B|* }0
3X-RAY DIFFRACTION3{ C|* }0

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