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- PDB-4u7t: Crystal structure of DNMT3A-DNMT3L in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 4u7t
TitleCrystal structure of DNMT3A-DNMT3L in complex with histone H3
Components
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • peptide from Histone H3.3
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / DNA methyltransferase / active form / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / genomic imprinting / negative regulation of chromosome condensation ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by heterochromatin formation / negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / genomic imprinting / negative regulation of chromosome condensation / DNA (cytosine-5-)-methyltransferase activity / Barr body / cellular response to bisphenol A / regulation of centromere complex assembly / unmethylated CpG binding / 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 / pericentric heterochromatin formation / inner kinetochore / ESC/E(Z) complex / XY body / muscle cell differentiation / cellular response to ethanol / response to vitamin A / oocyte maturation / nucleosomal DNA binding / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / hepatocyte apoptotic process / negative regulation of gene expression, epigenetic / nucleus organization / spermatid development / male meiosis I / chromosome, centromeric region / single fertilization / catalytic complex / subtelomeric heterochromatin formation / heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / enzyme activator activity / Condensation of Prophase Chromosomes / Transferases; Transferring one-carbon groups; Methyltransferases / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / post-embryonic development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / RNA Polymerase I Promoter Escape / cellular response to amino acid stimulus / placenta development / Transcriptional regulation by small RNAs / response to cocaine / Formation of the beta-catenin:TCF transactivating complex / response to lead ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / response to toxic substance / neuron differentiation / male gonad development / transcription corepressor activity / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / response to estradiol / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / spermatogenesis
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 ...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 / Vaccinia Virus protein VP39 / Zinc finger, FYVE/PHD-type / 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 / 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 / Histone H3.3 / DNA (cytosine-5)-methyltransferase 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsGuo, X. / Wang, L. / Yin, X. / Li, J. / Xiao, J. / He, S. / Wang, J. / Xu, Y.
CitationJournal: Nature / Year: 2015
Title: Structural insight into autoinhibition and histone H3-induced activation of DNMT3A
Authors: Guo, X. / Wang, L. / Li, J. / Ding, Z. / Xiao, J. / Yin, X. / He, S. / Shi, P. / Dong, L. / Li, G. / Tian, C. / Wang, J. / Cong, Y. / Xu, Y.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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 3A
B: DNA (cytosine-5)-methyltransferase 3-like
C: DNA (cytosine-5)-methyltransferase 3A
D: DNA (cytosine-5)-methyltransferase 3-like
F: peptide from Histone H3.3
G: peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,77414
Polymers152,6136
Non-polymers1,1618
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-15 kcal/mol
Surface area57470 Å2
Unit cell
Length a, b, c (Å)183.823, 183.823, 123.265
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain F
23chain G

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALchain AAA474 - 9127 - 445
21GLUGLUVALVALchain CCC474 - 9127 - 445
12PHEPHESERSERchain BBB177 - 3797 - 209
22PHEPHESERSERchain DDD177 - 3797 - 209
13ALAALASERSERchain FFE1 - 101 - 10
23ALAALASERSERchain GGF1 - 101 - 10

NCS ensembles :
ID
1
2
3
Detailsbiological unit is the same as asym.

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Components

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

#1: Protein DNA (cytosine-5)-methyltransferase 3A / DNA methyltransferases DNMT3A


Mass: 50878.434 Da / Num. of mol.: 2 / Fragment: UNP residues 476-912
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#2: Protein DNA (cytosine-5)-methyltransferase 3-like / DNA methyltransferases DNMT3L


Mass: 24119.654 Da / Num. of mol.: 2 / Fragment: UNP residues 178-379
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

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Protein/peptide , 1 types, 2 molecules FG

#3: Protein/peptide peptide from Histone H3.3 / histone H3 peptide


Mass: 1308.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 3 types, 19 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.02 Å3/Da / Density % sol: 69.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium Acetate, 0.6M Ammonium Sulfate / PH range: 5.3-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 9.9 % / Number: 519306 / Rmerge(I) obs: 0.095 / Χ2: 1.06 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 52477 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.245010.0411.1499.7
4.966.2410.0870.9949.8
4.334.9610.1071.06610
3.944.3310.1061.06410.1
3.653.9410.1111.0210
3.443.6510.141.05210
3.273.4410.2191.079.9
3.123.2710.3051.0519.8
33.1210.4691.069.8
2.9310.7211.0919.8
ReflectionResolution: 2.9→50 Å / Num. obs: 52477 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 77.28 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 139.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A1A, 2QRV

3a1a

2qrv


Resolution: 2.9→40.213 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 2667 5.09 %Random selection
Rwork0.223 49740 --
obs0.225 52407 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.66 Å2 / Biso mean: 83.463 Å2 / Biso min: 34.84 Å2
Refinement stepCycle: final / Resolution: 2.9→40.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9969 0 58 11 10038
Biso mean--61.11 60.49 -
Num. residues----1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110286
X-RAY DIFFRACTIONf_angle_d1.40813910
X-RAY DIFFRACTIONf_chiral_restr0.0561480
X-RAY DIFFRACTIONf_plane_restr0.0061792
X-RAY DIFFRACTIONf_dihedral_angle_d17.2873846
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3913X-RAY DIFFRACTION11.988TORSIONAL
12C3913X-RAY DIFFRACTION11.988TORSIONAL
21B1674X-RAY DIFFRACTION11.988TORSIONAL
22D1674X-RAY DIFFRACTION11.988TORSIONAL
31F80X-RAY DIFFRACTION11.988TORSIONAL
32G80X-RAY DIFFRACTION11.988TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8991-2.95180.40631390.36952548268797
2.9518-3.00860.39771560.320725892745100
3.0086-3.070.39041190.329826542773100
3.07-3.13670.35741370.301725772714100
3.1367-3.20960.41181270.29126372764100
3.2096-3.28990.32971300.282826262756100
3.2899-3.37880.32291370.302526102747100
3.3788-3.47820.32721310.263726112742100
3.4782-3.59040.31271440.263926382782100
3.5904-3.71860.27631560.241825892745100
3.7186-3.86740.30841490.243926212770100
3.8674-4.04320.27431310.213426142745100
4.0432-4.25620.21061550.203426272782100
4.2562-4.52250.20711430.178426142757100
4.5225-4.87110.22281310.17226392770100
4.8711-5.36030.18291230.185126522775100
5.3603-6.13360.26421500.207826392789100
6.1336-7.71870.25981520.210926282780100
7.7187-40.21730.2181570.19512627278498

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