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- PDB-6w8w: Crystal structure of mouse DNMT1 in complex with CCG DNA -

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Basic information

Entry
Database: PDB / ID: 6w8w
TitleCrystal structure of mouse DNMT1 in complex with CCG DNA
Components
  • CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
  • CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
  • DNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE/DNA / DNMT1 / protein-DNA complex / DNA methylation / 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 / PRC2 methylates histones and DNA / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / 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 / PRC2 methylates histones and DNA / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / S-adenosylmethionine metabolic process / female germ cell nucleus / methyl-CpG binding / DNA methylation-dependent constitutive heterochromatin formation / germ cell nucleus / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / heterochromatin / pericentric heterochromatin / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / replication fork / methyltransferase activity / nuclear estrogen receptor binding / promoter-specific chromatin binding / cellular response to amino acid stimulus / histone deacetylase binding / regulation of cell population proliferation / regulation of gene expression / methylation / response to xenobiotic stimulus / protein domain specific binding / 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 / enzyme binding / protein-containing complex / 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 / 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 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
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

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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: CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
E: CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')
D: CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
F: CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,79712
Polymers212,7676
Non-polymers1,0306
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-59 kcal/mol
Surface area74700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.794, 152.593, 95.631
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')


Mass: 3725.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')


Mass: 3677.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 68 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 0.1 M Sodium Citrate, 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 50826 / % possible obs: 98.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.274 / Rpim(I) all: 0.123 / Rrim(I) all: 0.302 / Χ2: 0.457 / Net I/σ(I): 1.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.114.41.03449940.3040.5171.1620.35796.8
3.11-3.234.80.8950220.5280.4330.9940.35898
3.23-3.384.80.71749860.6670.3510.8020.36697
3.38-3.565.70.58551140.8110.2620.6430.40398.9
3.56-3.785.80.47751250.8720.2120.5240.42799.1
3.78-4.075.70.33450830.9360.1490.3670.46498.5
4.07-4.4860.23650880.9670.1030.2580.51398.2
4.48-5.136.30.19151270.9790.0810.2070.5198.9
5.13-6.466.20.18250950.980.0780.1990.48498
6.46-506.50.08751920.9960.0360.0940.58998.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DA4

4da4


Resolution: 3→48.44 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.28 1996 3.93 %
Rwork0.2382 --
obs0.2398 50812 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 223.42 Å2 / Biso mean: 86.143 Å2 / Biso min: 26.97 Å2
Refinement stepCycle: final / Resolution: 3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12857 964 56 62 13939
Biso mean--82.57 49.66 -
Num. residues----1702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.060.38041250.36523081320687
3.06-3.140.37651350.34863481361698
3.14-3.240.37311370.3353507364498
3.24-3.340.35721520.30683453360597
3.34-3.460.34951390.28253551369099
3.46-3.60.28231380.2473541367999
3.6-3.760.28841600.25033489364999
3.76-3.960.29771460.24043528367499
3.96-4.210.24741470.21883477362497
4.21-4.530.24451400.19373565370599
4.53-4.990.26991480.19923535368399
4.99-5.710.28191380.22133490362898
5.71-7.190.23111430.22913568371199
7.19-48.440.23261480.20333550369897
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)
13.0834-1.0018-1.01072.4395-0.17651.05920.3305-0.3656-0.10890.5146-0.00111.012-0.416-0.4155-0.29361.12470.12670.3860.87850.17440.9698-16.3222-20.3219304.0181
23.31784.72580.68437.38041.05280.15970.296-0.3756-0.51440.5513-0.1304-0.69090.3770.1182-0.19940.820.0224-0.12840.50710.10360.536622.5044-33.9606295.9451
31.76610.21930.25442.8937-1.43412.4504-0.0512-0.0985-0.09020.50730.16240.0668-0.2271-0.2446-0.13390.7169-0.00520.05610.39980.0040.254411.3014-15.8613282.1126
41.8570.85390.88911.36090.92522.86040.00310.1323-0.0691-0.39250.1342-0.314-0.06290.2608-0.14170.49440.06050.07130.27870.03220.38534.3963-4.6378284.1278
52.25530.99541.12440.83370.5491.7969-0.0630.22140.1529-0.37730.11840.50170.1811-0.4993-0.091.0743-0.2083-0.23010.86570.22780.6987-15.493621.3042311.1772
68.1555-7.3333-1.55526.05791.49910.00790.414-0.39070.5592-0.48450.0174-0.8572-0.70580.5246-0.31090.8228-0.07320.08550.71440.09870.816933.408221.6241324.6321
71.46220.2642-0.08623.0516-1.40822.2433-0.130.04270.1036-0.27060.1946-0.09640.2591-0.2196-0.07230.7872-0.0235-0.01510.385-0.00110.29367.47816.8205334.3764
81.9951-0.7345-1.53781.47010.98942.6026-0.1422-0.19350.1480.62160.2264-0.34880.32010.2985-0.07230.55-0.0432-0.12740.34980.01670.377429.90042.9569337.5259
97.01173.12950.86624.2337-0.95143.12320.034-0.5372-0.67740.78790.78141.04110.7965-1.2622-1.04871.32180.05770.41260.95020.29791.274526.98884.7423295.0087
105.3168-2.62510.10414.87361.23320.5860.55240.59080.4195-0.28140.92921.4365-0.6303-1.7581-1.63961.3962-0.0165-0.21511.21680.56991.229724.4472-6.3785325.7876
112.47180.40261.87846.2941.57483.4062-0.6409-1.14960.1403-0.12680.34380.1462-0.04280.62850.03091.36740.00950.11550.98750.18371.010426.92564.6953292.7927
124.313-2.7063-1.40429.2452.49488.2013-0.73960.8786-0.28010.9858-0.2717-0.516-0.9451.39120.67031.5769-0.1028-0.04781.04350.27651.115924.0005-6.2112327.9796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 732 through 921 )A732 - 921
2X-RAY DIFFRACTION2chain 'A' and (resid 922 through 1023 )A922 - 1023
3X-RAY DIFFRACTION3chain 'A' and (resid 1024 through 1374 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1375 through 1600 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 732 through 938 )B732 - 938
6X-RAY DIFFRACTION6chain 'B' and (resid 939 through 983 )B939 - 983
7X-RAY DIFFRACTION7chain 'B' and (resid 984 through 1374 )B984 - 1374
8X-RAY DIFFRACTION8chain 'B' and (resid 1375 through 1600 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 12 )C1 - 12
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 12 )E1 - 12
11X-RAY DIFFRACTION11chain 'D' and (resid 13 through 24 )D13 - 24
12X-RAY DIFFRACTION12chain 'F' and (resid 13 through 24 )F13 - 24

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