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- PDB-5wvo: Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mo... -

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Basic information

Entry
Database: PDB / ID: 5wvo
TitleCrystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Histone H3.1
  • Ubiquitin
KeywordsSIGNALING PROTEIN/TRANSFERASE / DNA methylation / Ubiquitination / SIGNALING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / cellular response to bisphenol A / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / DNA methylation-dependent heterochromatin formation / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of gene expression via chromosomal CpG island methylation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / pericentric heterochromatin / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / telomere organization / Nuclear events stimulated by ALK signaling in cancer / Chromatin modifying enzymes / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / positive regulation of vascular associated smooth muscle cell proliferation / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / RNA Polymerase I Promoter Opening / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / Assembly of the ORC complex at the origin of replication / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / Interleukin-7 signaling / epigenetic regulation of gene expression / NF-kB is activated and signals survival / DNA methylation / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / Condensation of Prophase Chromosomes / HCMV Late Events / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / cellular response to amino acid stimulus / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs
Similarity search - Function
Arc Repressor Mutant, subunit A - #2230 / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site ...Arc Repressor Mutant, subunit A - #2230 / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1 / Ubiquitin-ribosomal protein eS31 fusion protein / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsIshiyama, S. / Nishiyama, A. / Nakanishi, M. / Arita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST PRESTO Japan
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance
Authors: Ishiyama, S. / Nishiyama, A. / Saeki, Y. / Moritsugu, K. / Morimoto, D. / Yamaguchi, L. / Arai, N. / Matsumura, R. / Kawakami, T. / Mishima, Y. / Hojo, H. / Shimamura, S. / Ishikawa, F. / ...Authors: Ishiyama, S. / Nishiyama, A. / Saeki, Y. / Moritsugu, K. / Morimoto, D. / Yamaguchi, L. / Arai, N. / Matsumura, R. / Kawakami, T. / Mishima, Y. / Hojo, H. / Shimamura, S. / Ishikawa, F. / Tajima, S. / Tanaka, K. / Ariyoshi, M. / Shirakawa, M. / Ikeguchi, M. / Kidera, A. / Suetake, I. / Arita, K. / Nakanishi, M.
History
DepositionDec 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: DNA (cytosine-5)-methyltransferase 1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1165
Polymers49,0514
Non-polymers651
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-22 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.362, 198.779, 76.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 2 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Plasmid: pET22b
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpT4 (others)
Strain (production host): BL21(DE3) / References: UniProt: P62979
#2: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / CXXC-type zinc finger protein 9 / DNA methyltransferase HsaI / M.HsaI / MCMT


Mass: 27980.334 Da / Num. of mol.: 1 / Fragment: RFTS domain, UNP residues 351-600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1, AIM, CXXC9, DNMT / Plasmid: modified pGEX4T vector
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpT4 (others)
Strain (production host): Rosetta2 (DE3)
References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase
#3: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 3824.465 Da / Num. of mol.: 1 / Fragment: UNP residues 2-37 / Mutation: K18C,K23C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Plasmid: modified pGEX4T
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpT4 (others)
Strain (production host): BL21(DE3) / References: UniProt: P68431
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.997→34.181 Å / Num. obs: 35892 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.778 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 3EPZ

1ubq

3epz


Resolution: 1.997→34.181 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2387 1855 5.17 %
Rwork0.1958 --
obs0.198 35890 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.997→34.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 1 197 3339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193237
X-RAY DIFFRACTIONf_angle_d0.9344378
X-RAY DIFFRACTIONf_dihedral_angle_d17.9121980
X-RAY DIFFRACTIONf_chiral_restr0.063496
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9969-2.05090.27231380.24562477X-RAY DIFFRACTION96
2.0509-2.11130.31641540.2452580X-RAY DIFFRACTION100
2.1113-2.17940.28961280.23122598X-RAY DIFFRACTION100
2.1794-2.25730.29821360.2262598X-RAY DIFFRACTION100
2.2573-2.34770.21991430.21632606X-RAY DIFFRACTION100
2.3477-2.45450.28141720.222585X-RAY DIFFRACTION100
2.4545-2.58380.30361370.2132597X-RAY DIFFRACTION100
2.5838-2.74570.24521470.21982612X-RAY DIFFRACTION100
2.7457-2.95750.28231510.21652634X-RAY DIFFRACTION100
2.9575-3.2550.24811310.20992641X-RAY DIFFRACTION100
3.255-3.72550.22761410.18212642X-RAY DIFFRACTION100
3.7255-4.69180.18741240.15252692X-RAY DIFFRACTION100
4.6918-34.1860.18891530.17412773X-RAY DIFFRACTION99

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