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- PDB-7lmm: Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 -

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Basic information

Entry
Database: PDB / ID: 7lmm
TitleCrystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2
Components
  • DNA (cytosine-5)-methyltransferase 1,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: 2.798 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,DNA (cytosine-5)-methyltransferase 1
B: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
C: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
D: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
F: Histone H4
G: Histone H4
I: Histone H4
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,93312
Polymers77,6718
Non-polymers2624
Water64936
1
A: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4833
Polymers19,4182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
G: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4833
Polymers19,4182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
I: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4833
Polymers19,4182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4833
Polymers19,4182
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.696, 80.281, 130.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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,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: 1645.932 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.: 36 / 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: 49.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→34.91 Å / Num. obs: 18810 / % possible obs: 99.5 % / Redundancy: 12.9 % / Biso Wilson estimate: 61.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1823 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WXX

4wxx


Resolution: 2.798→34.906 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1881 10 %
Rwork0.2066 --
obs0.2125 18807 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→34.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 4 36 5206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085298
X-RAY DIFFRACTIONf_angle_d0.9627214
X-RAY DIFFRACTIONf_dihedral_angle_d9.3353110
X-RAY DIFFRACTIONf_chiral_restr0.051785
X-RAY DIFFRACTIONf_plane_restr0.006923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.798-2.87340.34661380.3071246X-RAY DIFFRACTION97
2.8734-2.95790.40861430.29181290X-RAY DIFFRACTION100
2.9579-3.05340.34551410.27381266X-RAY DIFFRACTION100
3.0534-3.16240.33571400.2751259X-RAY DIFFRACTION98
3.1624-3.28890.26671430.2381289X-RAY DIFFRACTION100
3.2889-3.43850.28091460.24211305X-RAY DIFFRACTION100
3.4385-3.61960.31611420.22821287X-RAY DIFFRACTION100
3.6196-3.84610.28491470.20091313X-RAY DIFFRACTION100
3.8461-4.14260.30071430.19011292X-RAY DIFFRACTION99
4.1426-4.55870.21281460.17331308X-RAY DIFFRACTION100
4.5587-5.21650.20981470.15951328X-RAY DIFFRACTION100
5.2165-6.56510.22661480.18361340X-RAY DIFFRACTION99
6.5651-34.9060.24851570.20191403X-RAY DIFFRACTION99
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)
12.7979-2.20251.47333.79341.31673.77170.6262-0.2798-0.75440.22310.0319-0.72080.54750.0723-0.63870.52280.086-0.08680.6793-0.06410.80031.11113.637-22.117
27.3993-0.9977-1.42287.73930.15886.7593-0.4410.5534-0.4527-0.4732-0.27110.61760.7963-1.06370.41940.3226-0.08520.00760.3605-0.10250.3984-17.99212.386-30.55
37.77471.59663.61844.69631.95848.12510.1191-0.2045-0.11880.15980.0948-0.01690.39040.3181-0.1660.22920.00910.06170.3305-0.0720.2759-9.02817.46-20.508
47.34365.55552.06528.74181.15172.54110.1190.1207-0.7275-0.43540.6094-1.7444-0.69490.3221-0.55870.20540.06210.01730.3802-0.04620.4167-1.17625.3-19.089
51.91963.47261.34969.15390.82161.99110.2481-0.3002-0.23630.2191-0.2422-0.45530.1002-0.01530.09740.1963-0.01440.03350.4282-0.02690.306-5.32924.117-18.302
60.7495-0.4587-0.83013.18370.64986.1719-0.32220.1608-0.08790.52620.2061-0.3643-0.281-0.22190.15830.29960.0069-0.00830.4975-0.1660.3519-2.76444.10214.72
75.4693-3.5026-1.52896.6222.50675.4221-0.2546-0.1726-0.56531.0592-0.40390.63320.0944-0.24370.50930.5662-0.08480.05290.3497-0.10620.3519-12.05149.64531.291
85.4811.48212.44036.58332.69019.1686-0.9889-0.23481.16690.3771-0.2615-0.9608-1.18070.22831.08490.62830.082-0.19320.49290.21380.6381-0.25330.705-55.607
96.9366-1.87710.52934.70561.15574.1449-0.10680.22660.2771-0.3046-0.05420.6587-0.8413-0.24550.06140.51150.1381-0.0290.50720.1930.6388-12.427.855-60.526
103.1537-0.60251.3493.3406-2.29923.015-0.1890.57530.4819-0.1222-0.2268-0.2749-0.26830.37390.34090.32450.1474-0.00930.51350.22070.4671-5.55417.629-56.97
114.85161.5678-3.72014.5289-2.51373.4623-0.0615-0.9075-0.80230.3926-0.4974-0.15420.10140.35220.41040.4061-0.1333-0.0380.43820.04560.4769-6.178-9.21-73.741
123.95612.27292.05952.383-0.3357.6327-0.1065-0.27920.5294-0.84080.47931.17750.3214-0.6418-0.17130.4935-0.0707-0.06190.46020.0930.6292-13.113-16.361-84.875
133.08284.34740.20566.90460.88931.0215-0.34510.2119-0.947-0.89760.33520.657-0.3787-0.00320.00310.14660.13880.0470.4764-0.00990.8429-31.62413.459-19.14
147.75222.03591.11884.0210.08242.2567-0.1772-0.0385-0.86250.1660.14431.36130.3431-0.4974-0.00510.3707-0.03850.11560.57540.01550.9679-43.0715.286-15.724
155.41831.69220.02967.9353-0.60452.4963-0.2538-0.0215-0.6015-0.31720.0380.3810.1844-0.11560.13160.2189-0.0220.07290.31670.01460.4075-34.73124.194-17.385
162.2913-0.24062.60494.67680.15124.0296-0.0858-1.14380.04710.6464-0.26021.53690.1117-1.58320.27410.5794-0.01760.22080.7806-0.0550.6338-40.53626.202-8.306
174.06690.4836-1.53367.10574.89039.4556-0.29580.6263-0.2252-0.6907-1.09020.6437-1.8405-0.9910.77840.45820.0061-0.07850.686-0.12060.6616-40.01448.3561.1
183.6376-3.09920.79453.4331-2.2214.2090.1003-0.4761-0.28220.83970.03210.69650.7572-0.1297-0.17470.63150.0774-0.00820.4163-0.01980.379-33.13242.12523.228
198.9744-5.5897-2.10673.38991.20756.1343-0.41380.20480.12420.40650.49431.51710.1828-0.601-0.20430.4283-0.04130.05870.44460.0660.8556-47.75851.94126.063
206.27151.6137-5.36975.21570.06355.3075-0.11330.271.12810.80670.8188-1.1563-1.2582-0.8488-0.29430.8463-0.2307-0.16420.78680.27431.2124-38.0431.392-51.773
214.8115-2.06740.26456.3906-0.30444.0416-0.31670.34631.11790.10260.0765-0.8517-0.6715-0.20060.15350.505-0.0907-0.16490.4010.05580.6914-47.18624.012-52.726
224.35092.2147-0.7177.11261.06023.9471-0.59320.0533-0.5734-1.20660.251-0.21830.46680.19290.24650.63080.00970.13840.2469-0.04030.4069-47.238-14.292-86.666
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 728:740 )A728 - 740
3X-RAY DIFFRACTION3( CHAIN A AND RESID 741:782 )A741 - 782
4X-RAY DIFFRACTION4( CHAIN A AND RESID 783:809 )A783 - 809
5X-RAY DIFFRACTION5( CHAIN A AND RESID 810:834 )A810 - 834
6X-RAY DIFFRACTION6( CHAIN A AND RESID 835:875 )A835 - 875
7X-RAY DIFFRACTION7( CHAIN A AND RESID 876:897 )A876 - 897
8X-RAY DIFFRACTION8( CHAIN B AND RESID 725:727 )B725 - 727
9X-RAY DIFFRACTION9( CHAIN B AND RESID 728:782 )B728 - 782
10X-RAY DIFFRACTION10( CHAIN B AND RESID 783:839 )B783 - 839
11X-RAY DIFFRACTION11( CHAIN B AND RESID 840:867 )B840 - 867
12X-RAY DIFFRACTION12( CHAIN B AND RESID 868:897 )B868 - 897
13X-RAY DIFFRACTION13( CHAIN C AND RESID 725:727 )C725 - 727
14X-RAY DIFFRACTION14( CHAIN C AND RESID 728:782 )C728 - 782
15X-RAY DIFFRACTION15( CHAIN C AND RESID 783:824 )C783 - 824
16X-RAY DIFFRACTION16( CHAIN C AND RESID 825:834 )C825 - 834
17X-RAY DIFFRACTION17( CHAIN C AND RESID 835:862 )C835 - 862
18X-RAY DIFFRACTION18( CHAIN C AND RESID 863:874 )C863 - 874
19X-RAY DIFFRACTION19( CHAIN C AND RESID 875:897 )C875 - 897
20X-RAY DIFFRACTION20( CHAIN D AND RESID 725:727 )D725 - 727
21X-RAY DIFFRACTION21( CHAIN D AND RESID 728:839 )D728 - 839
22X-RAY DIFFRACTION22( CHAIN D AND RESID 840:897 )D840 - 897

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