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- PDB-8v9u: Solution NMR structure of human DNMT1 N-terminal alpha-helical domain -

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Basic information

Entry
Database: PDB / ID: 8v9u
TitleSolution NMR structure of human DNMT1 N-terminal alpha-helical domain
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / DNMT1 / DNA methylation / epigenetics / gene expression / transcription / DNA damage repair
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. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type 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
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHu, Q. / Botuyan, M.V. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: To Be Published
Title: Solution NMR structure of human DNMT1 N-terminal alpha-helical domain
Authors: Hu, Q. / Botuyan, M.V. / Mer, G.
History
DepositionDec 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,4951
Polymers9,4951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9494.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1, AIM, CXXC9, DNMT / Plasmid: pTEV / Production host: Escherichia coli (E. coli)
References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1212isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D HN(CA)CB
181isotropic13D CBCA(CO)NH
1161isotropic13D (H)CCH-COSY
1173isotropic13D (H)CCH-COSY
1111isotropic13D (H)CCH-TOCSY
1183isotropic13D (H)CCH-TOCSY
1131isotropic13D HBHA(CO)NH
1141isotropic13D 1H-13C NOESY
1153isotropic13D 1H-13C NOESY
1202isotropic13D 1H-15N NOESY
1191isotropic13D 1H-15N NOESY
1224anisotropic12D 1H-15N IPAP HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2ODNMT1 was in 20 mM MES/Bis-Tris, 50 mM NaCl, pH 6.0.15N_13C_sample90% H2O/10% D2O
solution31 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 100% D2ODNMT1 was in 20 mM MES/Bis-Tris, 50 mM NaCl, pH 6.0.15N_13C_sample100% D2O
solution21 mM [U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2ODNMT1 was in 20 mM MES/Bis-Tris, 50 mM NaCl, pH 6.0.15N_sample90% H2O/10% D2O
solution41 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% D2ODNMT1 was in 20 mM MES/Bis-Tris, 50 mM NaCl, pH 6.0.15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNMT1[U-13C; U-15N]1
20 mMMES/Bis-Trisnatural abundance1
50 mMsodium chloridenatural abundance1
1 mMDNMT1[U-13C; U-15N]3
20 mMMES/Bis-Trisnatural abundance3
50 mMsodium chloridenatural abundance3
1 mMDNMT1[U-15N]2
20 mMMES/Bis-Trisnatural abundance2
50 mMsodium chloridenatural abundance2
1 mMDNMT1[U-15N]4
20 mMMES/Bis-Trisnatural abundance4
50 mMsodium chloridenatural abundance4
5 %pentaethylene glycol monododecyl ether (C12E5)natural abundance4
95 %n-hexanolnatural abundance4
Sample conditionsIonic strength: 50 mM / Label: Conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS+Shen, Delaglio, Cornilescu and Baxgeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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