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- PDB-6w8v: Crystal structure of mouse DNMT1 in complex with ACG DNA -

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Basic information

Entry
Database: PDB / ID: 6w8v
TitleCrystal structure of mouse DNMT1 in complex with ACG DNA
Components
  • ACG DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3')
  • ACG DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3')
  • DNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE/DNA / DNA methylation / DNMT1 / epigenetics / TRANSFERASE / TRANSFERASE-DNA complex
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 / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase ...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 / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / 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 / pericentric heterochromatin / 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
DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. ...DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / : / 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 / DNA (> 10) / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsAnteneh, H. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2020
Title: DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context
Authors: Adam, S. / Anteneh, H. / Hornisch, M. / Wagner, V. / Lu, J. / Radde, N.E. / Bashtrykov, P. / Song, J. / Jeltsch, A.
History
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: DNA (cytosine-5)-methyltransferase 1
C: ACG DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3')
E: ACG DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3')
D: ACG DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3')
F: ACG DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,79712
Polymers212,7676
Non-polymers1,0306
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-76 kcal/mol
Surface area75050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 152.149, 96.049
Angle α, β, γ (deg.)90.000, 94.290, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 732 through 733 and (name N...
21(chain B and (resid 732 through 750 or (resid 751...
12chain C
22chain E
13chain D
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPARGARG(chain A and ((resid 732 through 733 and (name N...AA732 - 7333 - 4
121ASPASPZNZN(chain A and ((resid 732 through 733 and (name N...AA - I732 - 17033
131ASPASPZNZN(chain A and ((resid 732 through 733 and (name N...AA - I732 - 17033
141ASPASPZNZN(chain A and ((resid 732 through 733 and (name N...AA - I732 - 17033
151ASPASPZNZN(chain A and ((resid 732 through 733 and (name N...AA - I732 - 17033
211ASPASPTYRTYR(chain B and (resid 732 through 750 or (resid 751...BB732 - 7503 - 21
221GLNGLNGLNGLN(chain B and (resid 732 through 750 or (resid 751...BB75122
231ASPASPZNZN(chain B and (resid 732 through 750 or (resid 751...BB - L732 - 17033
241ASPASPZNZN(chain B and (resid 732 through 750 or (resid 751...BB - L732 - 17033
251ASPASPZNZN(chain B and (resid 732 through 750 or (resid 751...BB - L732 - 17033
261ASPASPZNZN(chain B and (resid 732 through 750 or (resid 751...BB - L732 - 17033
271ASPASPZNZN(chain B and (resid 732 through 750 or (resid 751...BB - L732 - 17033
112DCDCDTDTchain CCC1 - 121 - 12
212DCDCDTDTchain EED1 - 121 - 12
113DADADGDGchain DDE13 - 241 - 12
213DADADGDGchain FFF13 - 241 - 12

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 98980.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Production host: Escherichia coli (E. coli)
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: DNA chain ACG DNA (5'-D(*CP*CP*TP*TP*CP*(5CM)P*GP*TP*AP*AP*GP*T)-3')


Mass: 3627.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain ACG DNA (5'-D(*AP*CP*TP*TP*AP*(C49)P*GP*GP*AP*AP*GP*G)-3')


Mass: 3775.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate pH 4.8, 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 45209 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.393 / Rpim(I) all: 0.164 / Rrim(I) all: 0.426 / Χ2: 0.518 / Net I/σ(I): 1.6 / Num. measured all: 301241
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.1-3.215.92.06345230.3070.9252.2670.42
3.21-3.346.41.55244580.5320.6641.690.422
3.34-3.496.51.20345200.6730.511.3090.466
3.49-3.687.10.87445430.780.3510.9420.498
3.68-3.917.10.6644590.8980.2660.7120.517
3.91-4.2170.44345210.9470.180.4780.472
4.21-4.636.50.29245260.9640.1240.3180.502
4.63-5.36.50.2545280.9730.1060.2720.501
5.3-6.677.10.2345190.9810.0920.2480.516
6.67-506.60.10146120.9960.0430.110.843

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DA4

4da4


Resolution: 3.12→48.471 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 2000 4.44 %
Rwork0.2457 43087 -
obs0.2471 45087 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.31 Å2 / Biso mean: 80.6753 Å2 / Biso min: 29.15 Å2
Refinement stepCycle: final / Resolution: 3.12→48.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12910 978 56 0 13944
Biso mean--81.61 --
Num. residues----1704
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5032X-RAY DIFFRACTION5.04TORSIONAL
12B5032X-RAY DIFFRACTION5.04TORSIONAL
21C220X-RAY DIFFRACTION5.04TORSIONAL
22E220X-RAY DIFFRACTION5.04TORSIONAL
31D220X-RAY DIFFRACTION5.04TORSIONAL
32F220X-RAY DIFFRACTION5.04TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.12-3.19780.41381260.3688272987
3.1978-3.28430.37521430.3515304999
3.2843-3.38090.3391420.32673079100
3.3809-3.490.32611450.31143105100
3.49-3.61470.34571430.28633095100
3.6147-3.75940.34741440.29563103100
3.7594-3.93040.28781430.26893094100
3.9304-4.13750.29151440.24483083100
4.1375-4.39660.26731440.21553129100
4.3966-4.73580.22881450.20383111100
4.7358-5.21180.25921440.20783110100
5.2118-5.96480.2341450.21823122100
5.9648-7.51060.23051460.21583121100
7.5106-48.4710.23261460.20293157100
Refinement TLS params.

Method: refined / 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)Origin x (Å)Origin y (Å)Origin z (Å)
12.48820.17551.29540.85910.13271.6949-0.5772-0.11850.8795-0.1454-0.0128-0.0001-0.52480.26630.43711.03820.0735-0.34870.4701-0.01640.73322.5830.6016203.9905
22.11380.14060.74291.89570.81272.7179-0.21860.1108-0.06980.12430.1297-0.04580.49550.4810.04180.83640.058-0.03810.45420.05570.26020.28718.237190.9335
31.8143-0.0295-0.12141.3283-0.7292.3211-0.24280.20.1749-0.8990.2160.55590.3599-0.41590.0210.74340.0026-0.19490.4463-0.03450.3825-26.49977.1026187.6931
40.90380.6219-0.4431.99960.36031.82840.02430.2297-0.1777-0.58840.0872-1.0213-0.34910.7128-0.21850.7477-0.13240.34850.9903-0.02861.036619.666-17.5901221.5466
52.9499-4.31950.43886.7786-1.06510.5382-0.00490.3376-0.6275-0.2722-0.08710.96180.3937-0.39240.08040.6824-0.02090.02850.535-0.10690.6813-24.372-23.3013229.6635
61.4524-0.3971-0.20223.210.86052.0246-0.1573-0.0867-0.23770.0827-0.0530.1069-0.15440.20220.18380.3922-0.00170.0160.3990.08380.3188-7.5697-14.7235242.073
71.6004-0.2522-0.0482.1588-0.74752.5252-0.1326-0.0816-0.09370.84340.17730.6439-0.4954-0.4380.00150.49920.04340.13830.42970.0040.4433-30.3179-0.4908241.2973
86.96212.59560.34492.8421.47882.9978-0.03460.2944-0.2166-0.71471.1956-1.0286-0.95731.5523-1.38881.4616-0.1016-0.24630.9593-0.24821.1577-20.9153-2.329199.396
94.4693-0.52342.67098.22120.64562.4327-0.1030.5343-0.07710.54140.7565-1.3560.17751.4327-0.60761.10240.1698-0.02240.8499-0.10341.0096-23.03218.9857230.423
105.92421.5436-0.98024.9196-1.67483.9381-0.9313-0.7618-0.462-0.8778-0.12640.57480.6193-0.56941.22181.47370.1755-0.08541.0313-0.19440.9261-20.5773-1.7785197.9208
116.4226-2.0922-0.07572.18281.5735.7738-0.11370.6710.28720.6067-0.25470.6361-0.387-0.97410.37071.23440.0015-0.02630.8251-0.12740.7854-22.97038.2229232.1231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 732 through 1147 )A732 - 1147
2X-RAY DIFFRACTION2chain 'A' and (resid 1148 through 1374 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1375 through 1600 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 732 through 924 )B732 - 924
5X-RAY DIFFRACTION5chain 'B' and (resid 925 through 995 )B925 - 995
6X-RAY DIFFRACTION6chain 'B' and (resid 996 through 1374 )B996 - 1374
7X-RAY DIFFRACTION7chain 'B' and (resid 1375 through 1600 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 12 )C1 - 12
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 12 )E1 - 12
10X-RAY DIFFRACTION10chain 'D' and (resid 13 through 24 )D13 - 24
11X-RAY DIFFRACTION11chain 'F' and (resid 13 through 24 )F13 - 24

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