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- PDB-4qbr: Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 p... -

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Basic information

Entry
Database: PDB / ID: 4qbr
TitleCrystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide
Components
  • DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
  • Histone H3
KeywordsTRANSFERASE / Zinc Finger / Histone Binding
Function / homology
Function and homology information


: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity ...: / positive regulation of cellular response to hypoxia / : / epigenetic programming of gene expression / cellular response to bisphenol A / protein-cysteine methyltransferase activity / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / XY body / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / cellular response to ethanol / response to vitamin A / : / response to ionizing radiation / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / heterochromatin / Chromatin modifying enzymes / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / response to cocaine / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / cellular response to amino acid stimulus / Transcriptional regulation by small RNAs / response to lead ion / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / neuron differentiation / response to toxic substance / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / 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 / response to estradiol / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / 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 / membrane / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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 3A, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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: 1.902 Å
AuthorsWang, H. / Li, H.
CitationJournal: To be Published
Title: Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs
Authors: Noh, K. / Wang, H. / Kim, H. / Wenderski, W. / Fang, F. / Li, C. / Dewell, S. / Wu, X. / Ferris, A. / Hughes, S.H. / Zheng, D. / Melnick, A.M. / Patel, D.J. / Li, H. / Allis, C.D.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3A
P: Histone H3
C: DNA (cytosine-5)-methyltransferase 3A
E: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,30210
Polymers32,9104
Non-polymers3926
Water3,891216
1
A: DNA (cytosine-5)-methyltransferase 3A
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6515
Polymers16,4552
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-0 kcal/mol
Surface area7660 Å2
MethodPISA
2
C: DNA (cytosine-5)-methyltransferase 3A
E: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6515
Polymers16,4552
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-0 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.057, 37.161, 50.125
Angle α, β, γ (deg.)78.70, 83.89, 81.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 15678.026 Da / Num. of mol.: 2 / Fragment: ADD Domain, UNP residues 476-611 / Mutation: G550D
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/peptide Histone H3 /


Mass: 776.881 Da / Num. of mol.: 2 / Fragment: H3 N-terminal / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE ENTITY 2 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE ...THE SEQUENCE OF THE ENTITY 2 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG3350, 0.1M Bis-Tris-HCL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19077 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.096
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.93196
1.93-1.97195.8
1.97-2.01196.5
2.01-2.05196.2
2.05-2.09196.4
2.09-2.14196.4
2.14-2.19196.2
2.19-2.25196.4
2.25-2.32196.9
2.32-2.39197.1
2.39-2.48196.2
2.48-2.58197.3
2.58-2.7196.9
2.7-2.84197
2.84-3.02197.7
3.02-3.25197.2
3.25-3.58197.4
3.58-4.09197.7
4.09-5.16194.5
5.16-50199.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→36.136 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 979 5.13 %
Rwork0.1779 --
obs0.1802 19072 96.52 %
all-19758 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→36.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 6 216 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082308
X-RAY DIFFRACTIONf_angle_d1.0933112
X-RAY DIFFRACTIONf_dihedral_angle_d14.472866
X-RAY DIFFRACTIONf_chiral_restr0.043326
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9017-2.0020.28951410.20522544X-RAY DIFFRACTION95
2.002-2.12740.23421440.18362541X-RAY DIFFRACTION96
2.1274-2.29160.25261270.17142601X-RAY DIFFRACTION96
2.2916-2.52220.24081470.17352595X-RAY DIFFRACTION97
2.5222-2.8870.23951460.18962589X-RAY DIFFRACTION97
2.887-3.63680.21461390.17482624X-RAY DIFFRACTION97
3.6368-36.14210.19691350.17192599X-RAY DIFFRACTION97

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