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- PDB-7lmk: Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 -

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Basic information

Entry
Database: PDB / ID: 7lmk
TitleCrystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Histone H4
KeywordsTRANSFERASE / DNA methylation / DNA methyltransferase 1 / Histone modification / Allosteric regulation
Function / homology
Function and homology information


: / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...: / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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. / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H4 / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.647 Å
AuthorsRen, W. / 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: 2021
Title: DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.
Authors: Ren, W. / Fan, H. / Grimm, S.A. / Kim, J.J. / Li, L. / Guo, Y. / Petell, C.J. / Tan, X.F. / Zhang, Z.M. / Coan, J.P. / Yin, J. / Kim, D.I. / Gao, L. / Cai, L. / Khudaverdyan, N. / Cetin, B. ...Authors: Ren, W. / Fan, H. / Grimm, S.A. / Kim, J.J. / Li, L. / Guo, Y. / Petell, C.J. / Tan, X.F. / Zhang, Z.M. / Coan, J.P. / Yin, J. / Kim, D.I. / Gao, L. / Cai, L. / Khudaverdyan, N. / Cetin, B. / Patel, D.J. / Wang, Y. / Cui, Q. / Strahl, B.D. / Gozani, O. / Miller, K.M. / O'Leary, S.E. / Wade, P.A. / Wang, G.G. / Song, J.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DNA (cytosine-5)-methyltransferase 1
D: DNA (cytosine-5)-methyltransferase 1
F: Histone H4
G: Histone H4
H: Histone H4
I: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,99312
Polymers77,7318
Non-polymers2624
Water54030
1
A: DNA (cytosine-5)-methyltransferase 1
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4983
Polymers19,4332
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 1
G: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4983
Polymers19,4332
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (cytosine-5)-methyltransferase 1
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4983
Polymers19,4332
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (cytosine-5)-methyltransferase 1
I: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4983
Polymers19,4332
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.060, 81.372, 129.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
DNA (cytosine-5)-methyltransferase 1 / Dnmt1


Mass: 17771.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DNMT1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q24K09, DNA (cytosine-5-)-methyltransferase
#2: Protein/peptide
Histone H4 /


Mass: 1660.966 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.647→81.37 Å / Num. obs: 22223 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 77.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 2.65→2.78 Å / Num. unique obs: 2882 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXX

4wxx


Resolution: 2.647→71.06 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1998 9.03 %
Rwork0.2058 20121 -
obs0.2106 22119 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.67 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.647→71.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 4 30 5147
Biso mean--68.82 66.85 -
Num. residues----657
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6474-2.71360.34871300.3289131591
2.7136-2.7870.33371410.3343141199
2.787-2.8690.36241430.30471434100
2.869-2.96160.33311440.3218145499
2.9616-3.06750.30561400.2802140798
3.0675-3.19030.29721420.2708144099
3.1903-3.33550.30231430.23841433100
3.3355-3.51130.29411450.24361454100
3.5113-3.73130.28911420.2252143798
3.7313-4.01940.22351440.19671453100
4.0194-4.42380.21881440.1789144699
4.4238-5.06380.21681430.1513144497
5.0638-6.37920.24231470.1758147998
6.3792-71.060.25421500.1879151495
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)
12.00951.85212.84253.18542.79368.26270.1088-0.5903-0.2830.81010.5960.68171.2029-0.8558-0.4650.6778-0.2427-0.01490.89180.18540.940569.5214.58121.581
27.3146-2.04151.86215.9257-3.67078.3810.15910.0067-0.57480.4299-0.1847-0.43311.01050.57230.0230.590.02470.05350.3910.01360.532788.5113.58928.313
34.6254-2.22351.89596.7884-3.0554.16210.07510.3498-0.2534-0.28520.08380.29940.265-0.1226-0.10020.3933-0.01240.02410.4533-0.00380.322775.82723.79918.159
45.95732.4223-0.01726.173-2.18343.34620.02030.0154-0.4564-0.4247-0.1023-0.2327-0.1074-0.08270.12470.6163-0.0021-0.00340.3904-0.00480.475777.64547.287-24.608
53.74860.44732.09514.51981.26793.6869-0.0079-0.58680.37180.402-0.068-0.6579-0.76290.36790.09560.8151-0.2106-0.02440.832-0.08540.694381.17728.32260.069
63.8161-0.21050.48372.41830.92992.86980.0107-0.51790.41520.1206-0.2704-0.1032-0.3583-0.13210.11890.5399-0.1433-0.02930.6126-0.12840.485777.68119.15756.61
71.7253-2.49591.64675.0323-1.13084.7297-0.09710.483-0.22240.21780.0241-0.25840.39250.516-0.00080.55360.03540.00030.6372-0.01810.599781.992-14.17481.085
84.6849-3.5078-3.85223.42011.8323.7089-0.43640.16540.08730.65680.6845-0.1420.23170.3889-0.47070.712-0.0590.07860.582-0.03620.8196102.00615.47920.736
96.02821.6098-0.27971.47750.83859.3039-0.13350.4198-2.01140.41390.4032-0.74271.70731.15340.35530.81860.1050.00531.23680.27791.5368123.08210.19419.523
102.84233.1517-1.84363.3064-2.06181.472-0.00740.6086-1.4177-0.6002-1.1618-2.15260.76691.96770.9370.82460.28610.11971.07160.14131.2081120.26112.6316.912
119.1940.76263.05685.9134-2.44997.5629-0.25020.8722-0.4422-0.4129-0.1634-1.04580.59260.72920.44350.47790.06690.15780.5475-0.09750.6586109.09718.96413.426
128.6484-2.699-1.0643.87681.26571.43380.01230.2637-0.6996-0.0808-0.3271-0.44760.20880.30490.26820.51980.0340.04620.5701-0.01150.4958106.08324.19716.084
133.55381.38420.52755.6502-3.1656.9141-0.6412-0.21080.01890.04170.0489-1.49350.35681.17970.86010.6163-0.06210.14060.93320.09410.9692113.88439.3828.434
145.08231.9161-0.89264.1988-1.80498.09510.0960.34480.0732-0.42740.021-0.74030.28460.3654-0.15670.60580.05550.08940.5345-0.00880.6628112.26948.721-21.608
159.61720.9549-2.24625.3747-3.35192.1176-0.55840.37282.2303-0.18780.21270.2948-0.89570.34330.3381.1772-0.1495-0.28230.7281-0.04980.9137122.92433.20348.636
167.2572-4.0225-3.14549.81975.73946.6459-0.7617-1.6101-0.39321.31911.0907-0.80550.05080.4207-0.11540.98650.1173-0.11670.6831-0.10530.8697124.27825.8857.175
174.91956.31774.43178.3664.43527.79210.6284-0.48022.18830.85271.06223.41470.7035-2.00760.62890.87250.32320.24821.0294-0.17711.9696105.36524.8358.957
185.49013.52241.85997.22972.39643.5188-0.4462-0.20581.2603-0.49570.13371.478-0.9111-0.22190.22230.6920.0968-0.09560.5067-0.01020.7549115.23422.91151.228
196.61242.52080.88412.07972.62775.07650.2001-0.4692-0.5211.0538-0.1404-0.68710.18850.25-0.22450.7587-0.0173-0.02630.5520.04620.7664122.4665.37754.811
204.7175-1.1774-0.99735.80621.75034.7907-0.3585-0.5415-0.53861.18810.21490.16140.58180.11890.28890.77360.03310.04180.48150.05440.5973118.584-14.30586.229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 724:727 )A724 - 727
2X-RAY DIFFRACTION2( CHAIN A AND RESID 728:749 )A728 - 749
3X-RAY DIFFRACTION3( CHAIN A AND RESID 750:839 )A750 - 839
4X-RAY DIFFRACTION4( CHAIN A AND RESID 840:897 )A840 - 897
5X-RAY DIFFRACTION5( CHAIN B AND RESID 726:771 )B726 - 771
6X-RAY DIFFRACTION6( CHAIN B AND RESID 772:839 )B772 - 839
7X-RAY DIFFRACTION7( CHAIN B AND RESID 840:897 )B840 - 897
8X-RAY DIFFRACTION8( CHAIN C AND RESID 726:727 )C726 - 727
9X-RAY DIFFRACTION9( CHAIN C AND RESID 728:740 )C728 - 740
10X-RAY DIFFRACTION10( CHAIN C AND RESID 741:749 )C741 - 749
11X-RAY DIFFRACTION11( CHAIN C AND RESID 750:782 )C750 - 782
12X-RAY DIFFRACTION12( CHAIN C AND RESID 783:829 )C783 - 829
13X-RAY DIFFRACTION13( CHAIN C AND RESID 830:839 )C830 - 839
14X-RAY DIFFRACTION14( CHAIN C AND RESID 840:897 )C840 - 897
15X-RAY DIFFRACTION15( CHAIN D AND RESID 727:749 )D727 - 749
16X-RAY DIFFRACTION16( CHAIN D AND RESID 750:762 )D750 - 762
17X-RAY DIFFRACTION17( CHAIN D AND RESID 763:771 )D763 - 771
18X-RAY DIFFRACTION18( CHAIN D AND RESID 772:829 )D772 - 829
19X-RAY DIFFRACTION19( CHAIN D AND RESID 830:839 )D830 - 839
20X-RAY DIFFRACTION20( CHAIN D AND RESID 840:897 )D840 - 897

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