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- PDB-6kdl: Crystal structure of human DNMT3B-DNMT3L complex (I) -

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Basic information

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


epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...epigenetic programing of female pronucleus / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / chorionic trophoblast cell differentiation / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / transposable element silencing by heterochromatin formation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / male meiosis I / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / catalytic complex / heterochromatin / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / 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 / cytosol / cytoplasm
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
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: 3.274 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 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)113,4556
Polymers112,6864
Non-polymers7692
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-18 kcal/mol
Surface area42240 Å2
Unit cell
Length a, b, c (Å)192.932, 192.932, 50.041
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1005))
21(chain D and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1002))
12(chain B and (resid 178 through 179 or resid 181...
22(chain C and (resid 178 through 179 or resid 181...

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
111ARGARGARGARG(chain A and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1005))AA571 - 5724 - 5
121PROPROCYSCYS(chain A and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1005))AA574 - 6077 - 40
131GLUGLUHOHHOH(chain A and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1005))AA - G609 - 100542
211ARGARGARGARG(chain D and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1002))DD571 - 5724 - 5
221PROPROCYSCYS(chain D and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1002))DD574 - 6077 - 40
231GLUGLUHOHHOH(chain D and (resid 571 through 572 or resid 574 through 607 or resid 609 through 1002))DD - J609 - 100242
112METMETPHEPHE(chain B and (resid 178 through 179 or resid 181...BB178 - 1793 - 4
122THRTHRLYSLYS(chain B and (resid 178 through 179 or resid 181...BB181 - 2006 - 25
132GLUGLUPROPRO(chain B and (resid 178 through 179 or resid 181...BB202 - 27227 - 97
142PROPROPROPRO(chain B and (resid 178 through 179 or resid 181...BB27499
152PROPROALAALA(chain B and (resid 178 through 179 or resid 181...BB277 - 347102 - 172
162ASNASNTYRTYR(chain B and (resid 178 through 179 or resid 181...BB349 - 377174 - 202
212METMETPHEPHE(chain C and (resid 178 through 179 or resid 181...CC178 - 1793 - 4
222THRTHRLYSLYS(chain C and (resid 178 through 179 or resid 181...CC181 - 2006 - 25
232GLUGLUPROPRO(chain C and (resid 178 through 179 or resid 181...CC202 - 27227 - 97
242PROPROPROPRO(chain C and (resid 178 through 179 or resid 181...CC27499
252PROPROALAALA(chain C and (resid 178 through 179 or resid 181...CC277 - 347102 - 172
262ASNASNTYRTYR(chain C and (resid 178 through 179 or resid 181...CC349 - 377174 - 202

NCS ensembles :
ID
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 5.12 Å3/Da / Density % sol: 75.95 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20 mM Tris-HCl (pH 7.4), 200 mM NaCl, 5% glycerol, and 0.5 mM TCEP

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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: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→30 Å / Num. obs: 28675 / % possible obs: 98.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.61
Reflection shellResolution: 3.27→3.39 Å / Rmerge(I) obs: 0.446 / Num. unique obs: 1335 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 3.274→29.468 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.27
RfactorNum. reflection% reflection
Rfree0.2121 1333 4.65 %
Rwork0.179 --
obs0.1803 28671 89.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 229.5 Å2 / Biso min: 3.64 Å2
Refinement stepCycle: final / Resolution: 3.274→29.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7408 0 52 190 7650
Biso mean--67.03 43.38 -
Num. residues----912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1692X-RAY DIFFRACTION9.508TORSIONAL
12D1692X-RAY DIFFRACTION9.508TORSIONAL
21B994X-RAY DIFFRACTION9.508TORSIONAL
22C994X-RAY DIFFRACTION9.508TORSIONAL
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 (%)
3.2744-3.39120.295566126942
3.3912-3.52680.2877207368
3.5268-3.6870.2408122296697
3.687-3.8810.2274153307499
3.881-4.12360.21071410.1676299599
4.1236-4.44090.18461480.1424305299
4.4409-4.8860.17461410.1351303399
4.886-5.58890.19671600.15293036100
5.5889-7.02560.21671743014100
7.02560.2036151282693
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)
18.30732.24851.93069.1217-0.95820.712-0.3338-0.32941.1671-0.6230.6669-1.1123-1.78541.1707-0.4071.8991-0.2194-0.3731.45090.17812.297241.356341.4621-18.9346
21.1130.2265-0.74060.1674-0.14550.49280.19570.98741.37450.5171-0.0223-0.2071-0.4943-0.0889-0.18651.17540.307-0.54121.10230.27132.481814.235336.2426-23.7504
33.3485-0.88241.60926.481-0.61375.7766-0.04150.64330.1262-0.5779-0.05990.55570.1155-0.30070.13720.15620.0649-0.08120.54170.05740.180139.1491-1.4977-14.1492
44.2308-2.2403-3.03475.1974-1.08813.9899-0.3189-0.58161.010.02050.21080.5518-0.5189-0.30220.12760.27580.1814-0.15110.59760.05570.593933.310110.6102-6.3192
53.2743-1.41672.68472.6179-2.01512.6967-0.3481-1.0264-0.13180.33640.43220.7547-0.2078-0.8634-0.05290.38620.18140.11050.99680.00540.386935.23182.27026.5447
61.6585-0.94470.41571.5718-0.67653.3613-0.238-0.2322-0.08310.30820.1590.2015-0.1551-0.0738-0.00880.39320.11640.03440.63270.0116-0.020750.9809-3.43734.2519
75.5964-1.27530.68433.0612-0.02223.9370.0858-0.0464-0.15650.1239-0.2327-0.65870.19880.50560.15890.36510.181-0.09550.32750.07010.32683.3492-22.27670.5632
82.02640.07470.66520.7338-0.59412.88620.14340.4952-0.382-0.2492-0.1012-0.1140.19470.1345-0.12850.5450.2362-0.01970.6138-0.08670.011569.7344-16.2626-13.0623
94.7509-4.70183.75225.4198-3.89545.60330.1505-0.08920.40360.271-0.1115-0.60240.10120.64740.05960.69740.3031-0.24831.24650.46111.5684117.9331-31.638912.4355
108.23140.49710.6083.12252.37211.80690.32230.9721-0.13580.0407-0.3994-1.78210.77742.2301-0.36320.65170.31-0.06181.59420.37481.762118.2903-29.08740.7253
117.3343-2.7320.98522.5697-0.38464.34950.0662-0.07730.69980.2438-0.3249-1.5017-0.21920.86320.2590.35070.1031-0.25720.91050.4041.4085106.3323-21.5386.187
127.81331.40712.81092.97210.91915.6158-0.1486-0.70741.00060.50580.2123-0.26860.18740.931-0.0790.5860.0746-0.38421.06540.22041.3838109.1003-18.75317.3966
132.0605-0.8612-1.97280.36070.82591.93360.2204-0.62170.6260.30370.1924-1.0993-0.37340.4259-0.43021.0147-0.0881-0.59571.29290.14792.0682117.2457-15.46914.7135
144.1257-1.20662.6510.3567-0.84262.762-0.13250.0350.8029-0.30640.16570.161-0.6015-0.5160.39421.0540.5133-0.57351.1684-0.06531.721810.111930.9619-20.3034
153.667-1.7750.27523.7451-0.39070.0434-0.477-0.00870.72410.85620.45431.9106-1.2736-1.3818-0.26281.70530.7262-0.49331.2608-0.1652.49595.111636.2883-13.521
165.8303-3.04710.71623.8482-0.8523.0992-0.3085-0.04761.5532-0.2369-0.02490.1047-0.6893-0.24720.28720.66740.3063-0.54760.61030.02431.434924.302126.2972-14.0686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 340 through 352 )C340 - 352
2X-RAY DIFFRACTION2chain 'C' and (resid 353 through 379 )C353 - 379
3X-RAY DIFFRACTION3chain 'D' and (resid 571 through 639 )D571 - 639
4X-RAY DIFFRACTION4chain 'D' and (resid 640 through 703 )D640 - 703
5X-RAY DIFFRACTION5chain 'D' and (resid 704 through 759 )D704 - 759
6X-RAY DIFFRACTION6chain 'D' and (resid 760 through 853 )D760 - 853
7X-RAY DIFFRACTION7chain 'A' and (resid 571 through 725 )A571 - 725
8X-RAY DIFFRACTION8chain 'A' and (resid 726 through 853 )A726 - 853
9X-RAY DIFFRACTION9chain 'B' and (resid 178 through 205 )B178 - 205
10X-RAY DIFFRACTION10chain 'B' and (resid 206 through 228 )B206 - 228
11X-RAY DIFFRACTION11chain 'B' and (resid 229 through 321 )B229 - 321
12X-RAY DIFFRACTION12chain 'B' and (resid 322 through 338 )B322 - 338
13X-RAY DIFFRACTION13chain 'B' and (resid 339 through 379 )B339 - 379
14X-RAY DIFFRACTION14chain 'C' and (resid 178 through 206 )C178 - 206
15X-RAY DIFFRACTION15chain 'C' and (resid 207 through 217 )C207 - 217
16X-RAY DIFFRACTION16chain 'C' and (resid 218 through 339 )C218 - 339

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