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- PDB-6u91: Crystal structure of DNMT3B(Q772R)-DNMT3L in complex with CpGpT DNA -

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Basic information

Entry
Database: PDB / ID: 6u91
TitleCrystal structure of DNMT3B(Q772R)-DNMT3L in complex with CpGpT DNA
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • CpGpT DNA (25-MER)
KeywordsTransferase/DNA / DNMT3B / DNMT3L / DNA methylation / Methyltransferase / transferase-DNA complex / TRANSFERASE
Function / homology
Function and homology information


retrotransposon silencing by heterochromatin formation / : / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...retrotransposon silencing by heterochromatin formation / : / epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / negative regulation of DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / DNA methylation-dependent heterochromatin formation / ESC/E(Z) complex / : / negative regulation of gene expression, epigenetic / DNA metabolic process / male meiosis I / catalytic complex / heterochromatin / enzyme activator activity / DNA methylation / placenta development / PRC2 methylates histones and DNA / condensed nuclear chromosome / Defective pyroptosis / stem cell differentiation / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / spermatogenesis / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / DNMT3, cysteine rich ADD domain, GATA1-like 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99998872297 Å
AuthorsGao, L. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R35GM119721 United States
CitationJournal: To Be Published
Title: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Authors: Gao, L.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: CpGpT DNA (25-MER)
F: CpGpT DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,99811
Polymers130,1566
Non-polymers8425
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.344, 190.344, 49.644
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31

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Components

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DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules ADBC

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


Mass: 33215.477 Da / Num. of mol.: 2 / Mutation: Q772R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli) / Variant (production host): DE3
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 24163.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DNA (cytosine-5)-methyltransferase 3-like / Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Escherichia coli (E. coli) / Variant (production host): DE3 / References: UniProt: Q9UJW3

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain CpGpT DNA (25-MER)


Mass: 7698.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 37 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.99 Å3/Da / Density % sol: 69.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl (pH 8.0), 200 mM MgCl2, 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.99998872297→47.59 Å / Num. obs: 40256 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 64.1976072599 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.76
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.36 / Num. unique obs: 4048 / CC1/2: 0.704 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YX2

5yx2


Resolution: 2.99998872297→47.586 Å / SU ML: 0.367122545453 / Cross valid method: FREE R-VALUE / σ(F): 1.95924514285 / Phase error: 27.4475126822
RfactorNum. reflection% reflection
Rfree0.25910047627 2018 5.02252420419 %
Rwork0.214549750174 --
obs0.216782524271 40179 99.6948042281 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 75.9153995093 Å2
Refinement stepCycle: LAST / Resolution: 2.99998872297→47.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7493 1020 55 32 8600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004292201539378925
X-RAY DIFFRACTIONf_angle_d0.65271053563112350
X-RAY DIFFRACTIONf_chiral_restr0.04176685233311347
X-RAY DIFFRACTIONf_plane_restr0.003934915024711422
X-RAY DIFFRACTIONf_dihedral_angle_d21.39292019315078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.3849488320471400.3380456847092738X-RAY DIFFRACTION97.957794418
3.075-3.15810.3242604349841440.3039117869522670X-RAY DIFFRACTION99.1194082423
3.1581-3.2510.348993234031270.3039868383662729X-RAY DIFFRACTION99.7555012225
3.251-3.35590.3592913388311380.2859095476412758X-RAY DIFFRACTION99.89651604
3.3559-3.47590.3138953048921440.2531435207282709X-RAY DIFFRACTION99.8599929996
3.4759-3.6150.2826213808611460.2332525968852731X-RAY DIFFRACTION100
3.615-3.77940.2307102836151480.2088753583432765X-RAY DIFFRACTION99.9313893654
3.7794-3.97860.238722393111460.202430275552701X-RAY DIFFRACTION99.9648876404
3.9786-4.22770.264728574131560.1898961923062732X-RAY DIFFRACTION100
4.2277-4.55390.202341576771440.1688637385862730X-RAY DIFFRACTION99.9304589708
4.5539-5.01170.2122637588661480.172358630512734X-RAY DIFFRACTION99.9306518724
5.0117-5.73590.2636786602671350.1975313689372727X-RAY DIFFRACTION99.9650716032
5.7359-7.22260.2165313344721500.2151365394342726X-RAY DIFFRACTION99.8957971518
7.2226-47.5860.2559259992421520.1963533989332711X-RAY DIFFRACTION99.5826086957

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