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- PDB-6kdb: Crystal structure of human DNMT3B-DNMT3L in complex with DNA cont... -

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Basic information

Entry
Database: PDB / ID: 6kdb
TitleCrystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site
Components
  • DNA (25-MER)
  • DNA (cytosine-5)-methyltransferase 3-like
  • DNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE/DNA / DNMT3B / DNA methyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA 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 / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates ...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 / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase / autosome 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 / enzyme activator activity / 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 / placenta development / 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 / DNA (> 10) / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3-like
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.862 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 1, 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
E: DNA (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8518
Polymers128,0826
Non-polymers7692
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-51 kcal/mol
Surface area48030 Å2
Unit cell
Length a, b, c (Å)194.827, 194.827, 49.844
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 570 or resid 573 through 633...
21(chain D and (resid 570 or resid 573 through 633...
12(chain B and (resid 178 through 209 or resid 211...
22(chain C and (resid 178 through 209 or resid 211...
13(chain E and resid 423 through 446)
23(chain F and resid 423 through 446)

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
111METMETMETMET(chain A and (resid 570 or resid 573 through 633...AA5703
121ARGARGLYSLYS(chain A and (resid 570 or resid 573 through 633...AA573 - 6336 - 66
131ASNASNALAALA(chain A and (resid 570 or resid 573 through 633...AA635 - 66068 - 93
141GLYGLYHOHHOH(chain A and (resid 570 or resid 573 through 633...AA - I663 - 100596
211METMETMETMET(chain D and (resid 570 or resid 573 through 633...DD5703
221ARGARGLYSLYS(chain D and (resid 570 or resid 573 through 633...DD573 - 6336 - 66
231ASNASNALAALA(chain D and (resid 570 or resid 573 through 633...DD635 - 66068 - 93
241GLYGLYHOHHOH(chain D and (resid 570 or resid 573 through 633...DD - L663 - 100296
112METMETLEULEU(chain B and (resid 178 through 209 or resid 211...BB178 - 2093 - 34
122SERSERLYSLYS(chain B and (resid 178 through 209 or resid 211...BB211 - 29236 - 117
132HISHISSERSER(chain B and (resid 178 through 209 or resid 211...BB177 - 3792 - 204
142VALVALLYSLYS(chain B and (resid 178 through 209 or resid 211...BB338 - 350163 - 175
152TRPTRPTYRTYR(chain B and (resid 178 through 209 or resid 211...BB359 - 377184 - 202
212METMETLEULEU(chain C and (resid 178 through 209 or resid 211...CC178 - 2093 - 34
222SERSERLYSLYS(chain C and (resid 178 through 209 or resid 211...CC211 - 29236 - 117
232ASPASPPROPRO(chain C and (resid 178 through 209 or resid 211...CC294 - 310119 - 135
242GLNGLNTYRTYR(chain C and (resid 178 through 209 or resid 211...CC318 - 377143 - 202
113DCDCDGDG(chain E and resid 423 through 446)EE423 - 4462 - 25
213DCDCDGDG(chain F and resid 423 through 446)FF423 - 4462 - 25

NCS ensembles :
ID
1
2
3

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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: DNA chain DNA (25-MER)


Mass: 7697.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 316 / 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: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES (pH 5.6), 200 mM KCl, 10 mM MgSO4, 10% PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 48145 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 29.05
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.524 / Num. unique obs: 2592 / CC1/2: 0.807

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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: 2.862→29.615 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.01
RfactorNum. reflection% reflection
Rfree0.202 2211 5.03 %
Rwork0.1632 --
obs0.1641 43949 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 350.77 Å2 / Biso min: 19 Å2
Refinement stepCycle: final / Resolution: 2.862→29.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7626 1022 52 316 9016
Biso mean--38.16 54.63 -
Num. residues----988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1712X-RAY DIFFRACTION10.406TORSIONAL
12D1712X-RAY DIFFRACTION10.406TORSIONAL
21B1042X-RAY DIFFRACTION10.406TORSIONAL
22C1042X-RAY DIFFRACTION10.406TORSIONAL
31E474X-RAY DIFFRACTION10.406TORSIONAL
32F474X-RAY DIFFRACTION10.406TORSIONAL
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 (%)
2.862-2.92380.304975109938
2.9238-2.99180.305697136849
2.9918-3.06650.2444110187165
3.0665-3.14930.2263158261391
3.1493-3.24190.21121502920100
3.2419-3.34640.22311562892100
3.3464-3.46580.25351682883100
3.4658-3.60430.18741862853100
3.6043-3.76810.21581160.14112922100
3.7681-3.96630.2081770.14592878100
3.9663-4.21410.17021620.13182906100
4.2141-4.53850.17221140.11482945100
4.5385-4.99320.14921760.12122860100
4.9932-5.71130.16821120.14052917100
5.7113-7.17860.18791142957100
7.17860.2346140285499
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)
13.10351.32220.40473.1671-0.51813.3793-0.1-0.0413-0.35320.14960.05020.5830.1954-0.36630.09740.14-0.07670.10560.53360.02280.3525-61.872251.6478-3.6869
20.76470.3265-0.43211.8168-0.62172.0061-0.12150.58960.0697-0.30880.10790.3894-0.0013-0.0526-0.1220.3049-0.1484-0.07750.72860.02020.0303-49.345659.9211-17.7816
35.2363-3.73945.37994.6339-4.14776.84061.60753.5643-3.3907-4.55210.14430.94234.5282-0.3241-1.74842.9725-0.0746-0.34322.4984-0.5951.9651-51.509142.7951-31.3268
48.1076-2.60983.33058.766-6.10657.83360.01130.4223-2.2216-1.36860.8233-0.99333.10681.6342-0.90761.43870.3354-0.20741.6655-0.42572.0822-43.047440.2042-13.8649
57.423-5.5868-3.94215.94230.27816.2580.6539-0.1869-1.9642-0.07870.4078-1.94230.47180.2257-1.04592.12-0.2176-0.23911.6491-0.152.3735-16.389453.24790.3005
64.32685.80844.56649.01885.6954.97611.3374-1.9676-2.91273.1784-0.4503-4.08524.26074.7237-0.87412.4340.5927-0.52792.66980.24691.9732-11.13565.024215.7204
75.0166-2.99492.062.7299-3.57926.7075-0.6991-0.4512-0.9261-1.32520.1092-1.20710.49660.53490.56191.3521-0.1378-0.17651.11740.17291.5702-13.262957.4222-2.1871
85.5173-2.45283.2153.352-3.4533.695-2.1286-0.95760.15121.41610.6739-2.5694-0.3765-1.14391.45362.42890.1697-0.27412.34130.03482.8976-25.316143.9226-3.444
97.4468-2.32860.73144.2344-3.90964.0121-0.58211.4905-3.8124-1.6010.00611.56442.5571-4.78690.59681.964-0.6845-0.06022.7802-0.59822.6273-35.050842.0081-19.6438
104.8032-4.81670.09224.8414-0.23632.0155-0.23111.8916-1.2995-2.07410.04185.1998-0.261-3.29260.19462.2066-0.1439-0.63672.89090.30743.2388-53.458436.7928-25.6198
114.29580.593-0.29682.00840.3893.36270.05060.06190.2905-0.1295-0.0967-0.6032-0.26260.33510.08340.3817-0.19450.06740.30430.07270.3448-13.826379.4253-12.3279
121.9972-0.2832-0.83510.7507-0.12132.31920.2039-0.48290.40540.4268-0.1573-0.1509-0.01650.0167-0.12320.4555-0.2277-0.00860.5083-0.0569-0.0573-27.215272.70481.7409
132.71421.9046-3.11584.8761-3.11393.86260.03430.015-0.3429-0.05580.0873-0.4545-0.28450.7295-0.01790.5428-0.34220.27021.1410.28921.574622.788.5611-22.1851
148.71992.3753-2.631.75721.11255.0044-0.0861-0.412-0.60440.1009-0.0995-0.62170.04430.76420.10820.2441-0.18530.07140.68160.33691.189311.103280.8463-14.3219
156.3318-2.0866-0.34160.92331.10884.1981-0.20880.9207-1.8337-0.5673-0.1553-0.63690.68830.34860.44510.5228-0.07330.5030.9042-0.04711.48819.221870.9895-26.5032
165.1448-0.16520.64690.83360.69751.9519-0.26480.2978-1.7608-0.03920.1738-0.49530.41790.7440.16610.7401-0.04430.61041.13940.09612.061421.041573.3909-25.8864
175.2568-0.3359-4.14211.7336-1.26234.64830.1191-0.0854-0.5325-0.00450.0521-0.1050.479-0.6305-0.08770.7321-0.46430.4010.92880.06521.5364-88.197924.73886.2686
182.08493.3008-0.62885.4525-2.04175.1758-0.1237-0.0431-0.9529-0.0317-0.3388-0.49780.8575-0.09550.32420.5326-0.22470.38460.47290.03051.309-72.374428.87771.7435
190.96380.88331.65036.13330.47213.03230.4292-0.4133-0.90470.1142-0.3809-1.4390.72380.2350.01930.9034-0.21720.34480.98550.49671.9494-73.463419.929511.1459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 570 through 725 )D570 - 725
2X-RAY DIFFRACTION2chain 'D' and (resid 726 through 853 )D726 - 853
3X-RAY DIFFRACTION3chain 'E' and (resid 422 through 426 )E422 - 426
4X-RAY DIFFRACTION4chain 'E' and (resid 427 through 431 )E427 - 431
5X-RAY DIFFRACTION5chain 'E' and (resid 432 through 446 )E432 - 446
6X-RAY DIFFRACTION6chain 'F' and (resid 422 through 426 )F422 - 426
7X-RAY DIFFRACTION7chain 'F' and (resid 427 through 431 )F427 - 431
8X-RAY DIFFRACTION8chain 'F' and (resid 432 through 436 )F432 - 436
9X-RAY DIFFRACTION9chain 'F' and (resid 437 through 441 )F437 - 441
10X-RAY DIFFRACTION10chain 'F' and (resid 442 through 446 )F442 - 446
11X-RAY DIFFRACTION11chain 'A' and (resid 570 through 725 )A570 - 725
12X-RAY DIFFRACTION12chain 'A' and (resid 726 through 853 )A726 - 853
13X-RAY DIFFRACTION13chain 'B' and (resid 177 through 217 )B177 - 217
14X-RAY DIFFRACTION14chain 'B' and (resid 218 through 291 )B218 - 291
15X-RAY DIFFRACTION15chain 'B' and (resid 292 through 339 )B292 - 339
16X-RAY DIFFRACTION16chain 'B' and (resid 340 through 379 )B340 - 379
17X-RAY DIFFRACTION17chain 'C' and (resid 177 through 217 )C177 - 217
18X-RAY DIFFRACTION18chain 'C' and (resid 218 through 325 )C218 - 325
19X-RAY DIFFRACTION19chain 'C' and (resid 326 through 378 )C326 - 378

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