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- PDB-6kdp: Crystal structure of human DNMT3B-DNMT3L complex (II) -

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Basic information

Entry
Database: PDB / ID: 6kdp
TitleCrystal structure of human DNMT3B-DNMT3L complex (II)
Components
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / DNMT3B / DNA methyltransferase / complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / male meiosis I / catalytic complex / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / stem cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / NoRC negatively regulates rRNA expression / transcription corepressor activity / spermatogenesis / methylation / negative regulation of DNA-templated transcription / positive regulation of gene expression / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain 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. ...DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLin, C.-C. / Chen, Y.-P. / Yang, W.-Z. / Shen, C.-K. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B.
Authors: Lin, C.C. / Chen, Y.P. / Yang, W.Z. / Shen, J.C.K. / Yuan, H.S.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 3B
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3-like
D: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5478
Polymers112,6864
Non-polymers8614
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-12 kcal/mol
Surface area42890 Å2
Unit cell
Length a, b, c (Å)72.105, 234.066, 230.951
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / M.HsaIIIB


Mass: 32715.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 23627.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJW3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 4.32 Å3/Da / Density % sol: 71.55 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 2.7 M Sodium formate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→30 Å / Num. obs: 32961 / % possible obs: 98 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.19
Reflection shellResolution: 2.93→3.04 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 1981 / CC1/2: 0.962

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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: 5YX2

5yx2


Resolution: 2.93→29.804 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.244 1678 5.09 %
Rwork0.205 --
obs0.2071 32942 77.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.72 Å2 / Biso mean: 54.2803 Å2 / Biso min: 17.76 Å2
Refinement stepCycle: final / Resolution: 2.93→29.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7669 0 58 111 7838
Biso mean--39.18 36.8 -
Num. residues----942
LS refinement shell

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

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9303-3.01650.3232790.2717155547
3.0165-3.11370.359969172652
3.1137-3.22490.3402112187557
3.2249-3.35380.2517101203761
3.3538-3.50630.2633129223467
3.5063-3.69080.2707129244273
3.6908-3.92160.23861420.2012273282
3.9216-4.22360.22791530.195310692
4.2236-4.64720.20811900.1687330699
4.6472-5.31630.23391930.17883370100
5.3163-6.68550.24651830.20743398100
6.68550.2389198348398
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)
11.1494-0.00420.54252.1312-0.53311.84670.03350.10190.05030.0272-0.0847-0.189-0.23490.07820.02760.19530.0176-0.030.26870.01130.273-20.960228.193-22.8502
20.41220.27190.05692.22120.10020.7453-0.0311-0.0395-0.0925-0.017-0.0513-0.47390.06430.21420.04610.22870.0387-0.02450.36490.04130.3818-10.450311.3255-20.3596
31.2384-0.43880.78842.3171-0.34540.4081-0.17740.00090.64550.58230.0921-0.1026-0.8706-0.26210.12970.92380.0389-0.06350.4758-0.01270.6333-22.665865.0491-32.9488
41.3753-0.42130.30250.3481-0.25271.4369-0.34760.05140.5120.00130.0764-0.6434-1.11220.67810.00370.7514-0.1569-0.10870.36190.00620.5098-14.047157.976-30.7337
50.2397-0.74250.51812.17-1.53851.08450.00040.37210.208-0.4068-0.1936-0.57480.06740.82190.17220.6559-0.12660.10660.65670.09360.7145-11.897246.0231-47.3711
61.81340.020.49271.48710.18141.653-0.0936-0.1757-0.0840.0795-0.2864-0.566-0.22550.0340.11510.373-0.0498-0.01690.21070.010.3037-17.046745.6336-32.8537
71.9057-0.26250.35662.27820.96312.1552-0.4072-0.12250.08870.6027-0.22950.0359-0.28860.0440.11290.70250.04830.02840.2559-0.00190.2816-24.226652.0744-32.635
81.3065-0.91471.83571.7751-2.04494.31670.16990.404-0.46040.06840.10270.4174-0.3231-0.4071-0.1270.56470.0007-0.00110.29-0.00470.2725-28.188444.9817-44.1241
91.40480.33990.55271.11590.58251.1424-0.0344-0.02190.3127-0.07960.085-0.01-0.2402-0.0268-0.00350.59840.06980.05370.2790.030.3372-31.372151.7411-46.9944
103.98044.0326-1.33344.4212-1.46530.47330.07470.2589-0.10330.0286-0.3369-0.40320.15040.8744-0.04440.8794-0.0231-0.05340.54450.03470.3876-23.383445.9146-55.325
111.13980.8162-0.05931.22510.19330.1503-0.45950.06820.3159-0.09730.2582-0.2605-0.5418-0.56290.03871.08560.1014-0.1280.38730.00930.3691-26.849165.9581-39.0068
121.6358-0.6796-0.79113.19060.0230.756-0.0523-0.2519-0.78950.1069-0.0630.33431.0347-0.31250.12950.8644-0.13850.1270.4909-0.07410.587-21.0322-61.7244-37.4913
132.2137-0.1396-1.07632.40890.5371.4619-0.27910.6097-0.52280.2851-0.4090.71721.0453-0.93470.1180.4879-0.21870.17920.3159-0.14230.3836-25.0632-48.2404-38.5619
141.6696-0.0443-0.252.4416-1.46053.3986-0.2655-0.2546-0.13970.49490.0912-0.02310.3012-0.23380.17490.60030.03150.06970.3421-0.03740.2947-16.2857-50.8369-35.3726
152.5028-1.073-1.97761.56971.09853.4621-0.0529-0.0290.1026-0.27060.286-0.3973-0.05810.3574-0.070.3178-0.05730.03980.222-0.04390.2665-10.3324-43.1652-45.4603
162.02120.6789-1.9112.0414-0.10013.1391-0.21270.0160.3242-0.09330.29250.2971-0.0585-0.2775-0.01490.62850.05620.08720.26410.00160.2253-8.7633-46.5609-52.0773
171.34430.2882-0.67571.7706-0.5991.0878-0.44240.3548-0.64050.08540.08120.32850.5799-0.13840.01171.08680.01130.21860.4115-0.05330.4247-14.1107-61.6205-44.6938
180.98950.2492-0.43131.80670.58032.0207-0.08330.13710.03920.12340.0050.15510.2731-0.09260.02010.1931-0.01310.04740.2839-0.02280.2781-21.9813-27.7646-25.1581
190.69320.3068-0.03751.94040.790.4951-0.09160.13590.1163-0.1642-0.08160.34090.0418-0.34260.03150.17060.04510.01290.4126-0.04490.3943-32.8444-10.9232-23.5882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 570 through 725 )A570 - 725
2X-RAY DIFFRACTION2chain 'A' and (resid 726 through 853 )A726 - 853
3X-RAY DIFFRACTION3chain 'B' and (resid 179 through 205 )B179 - 205
4X-RAY DIFFRACTION4chain 'B' and (resid 206 through 244 )B206 - 244
5X-RAY DIFFRACTION5chain 'B' and (resid 245 through 255 )B245 - 255
6X-RAY DIFFRACTION6chain 'B' and (resid 256 through 270 )B256 - 270
7X-RAY DIFFRACTION7chain 'B' and (resid 271 through 291 )B271 - 291
8X-RAY DIFFRACTION8chain 'B' and (resid 292 through 315 )B292 - 315
9X-RAY DIFFRACTION9chain 'B' and (resid 316 through 339 )B316 - 339
10X-RAY DIFFRACTION10chain 'B' and (resid 340 through 360 )B340 - 360
11X-RAY DIFFRACTION11chain 'B' and (resid 361 through 379 )B361 - 379
12X-RAY DIFFRACTION12chain 'C' and (resid 178 through 228 )C178 - 228
13X-RAY DIFFRACTION13chain 'C' and (resid 229 through 270 )C229 - 270
14X-RAY DIFFRACTION14chain 'C' and (resid 271 through 291 )C271 - 291
15X-RAY DIFFRACTION15chain 'C' and (resid 292 through 315 )C292 - 315
16X-RAY DIFFRACTION16chain 'C' and (resid 316 through 353 )C316 - 353
17X-RAY DIFFRACTION17chain 'C' and (resid 354 through 379 )C354 - 379
18X-RAY DIFFRACTION18chain 'D' and (resid 570 through 725 )D570 - 725
19X-RAY DIFFRACTION19chain 'D' and (resid 726 through 853 )D726 - 853

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