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- PDB-3a1b: Crystal structure of the DNMT3A ADD domain in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 3a1b
TitleCrystal structure of the DNMT3A ADD domain in complex with histone H3
ComponentsDNA (cytosine-5)-methyltransferase 3A, Histone H3.1
KeywordsTRANSFERASE / Zinc-finger / Histone binding / Chromosomal protein / DNA damage / DNA repair / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphoprotein / Alternative promoter usage / Metal-binding / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


positive regulation of cellular response to hypoxia / cellular response to bisphenol A / regulatory ncRNA-mediated heterochromatin formation / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins ...positive regulation of cellular response to hypoxia / cellular response to bisphenol A / regulatory ncRNA-mediated heterochromatin formation / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / XY body / response to vitamin A / cellular response to ethanol / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / catalytic complex / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / response to cocaine / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / cellular response to amino acid stimulus / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / response to lead ion / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / neuron differentiation / PKMTs methylate histone lysines / Meiotic recombination / response to toxic substance / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to estradiol / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / methylation / cadherin binding / response to xenobiotic stimulus / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / DNA (cytosine-5-)-methyltransferase, N-terminal / 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. ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H3.1 / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.292 Å
AuthorsOtani, J. / Arita, K. / Ariyoshi, M. / Shirakawa, M.
CitationJournal: Embo Rep. / Year: 2009
Title: Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain
Authors: Otani, J. / Nankumo, T. / Arita, K. / Inamoto, S. / Ariyoshi, M. / Shirakawa, M.
History
DepositionMar 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A, Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,70411
Polymers18,0731
Non-polymers63110
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.547, 68.547, 109.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A, Histone H3.1 / Dnmt3a / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA / H3/a / H3/b / H3/c / H3/d ...Dnmt3a / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA / H3/a / H3/b / H3/c / H3/d / H3/f / H3/h / H3/i / H3/j / H3/k / H3/l


Mass: 18072.805 Da / Num. of mol.: 1
Fragment: ADD(ATRX-DNMT3-DNMT3L) domain(residues 476-614), UNP residues 2-21(Histone H3.1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P68431, UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 3.57 Å3/Da / Density % sol: 65.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.292→32.721 Å / Num. all: 12159 / Num. obs: 12159 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 24.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15
Reflection shellResolution: 2.292→2.38 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.428 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A1A

3a1a


Resolution: 2.292→32.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.047 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22408 576 4.8 %RANDOM
Rwork0.19198 ---
obs0.19344 11534 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.685 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2--2.16 Å20 Å2
3----4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.292→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 31 38 1242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221219
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9611627
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8545150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22923.44361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94615212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5771512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02927
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2815
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.5761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27721177
X-RAY DIFFRACTIONr_scbond_it2.2823523
X-RAY DIFFRACTIONr_scangle_it3.574.5448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.292→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 32 -
Rwork0.232 695 -
obs--82.9 %
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)
114.2058-3.441-1.086715.1387-8.145.01940.70170.1273-1.8014-0.6157-1.0545-0.92251.36540.59340.35280.23260.15870.26660.3778-0.00530.074234.0369-7.275211.638
21.9657-1.76262.53455.4161-4.77957.3528-0.0322-0.2025-0.1149-0.10920.06660.05960.2174-0.3244-0.03440.0650.03020.00890.12460.0220.067721.09660.931313.6057
34.294-0.4647-1.55977.3807-2.531910.8445-0.2171-0.22790.34390.2288-0.1787-0.8617-0.60851.08760.39570.15280.003-0.10750.21450.0970.182731.35455.341217.7805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A456 - 472
2X-RAY DIFFRACTION2A473 - 543
3X-RAY DIFFRACTION3A544 - 610

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