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- PDB-5ydr: Structure of DNMT1 RFTS domain in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5ydr
TitleStructure of DNMT1 RFTS domain in complex with ubiquitin
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Polyubiquitin-B
KeywordsPROTEIN BINDING/TRANSFERASE / DNA methylation / PROTEIN BINDING / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


histone H3K23ub reader activity / histone H3K18ub reader activity / histone H3K14ub reader activity / : / epigenetic programming of gene expression / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase ...histone H3K23ub reader activity / histone H3K18ub reader activity / histone H3K14ub reader activity / : / epigenetic programming of gene expression / chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / female germ cell nucleus / SUMOylation of DNA methylation proteins / STAT3 nuclear events downstream of ALK signaling / methyl-CpG binding / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / DNA methylation-dependent constitutive heterochromatin formation / seminiferous tubule development / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / energy homeostasis / heterochromatin / neuron projection morphogenesis / Nuclear events stimulated by ALK signaling in cancer / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of neuron apoptotic process / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / positive regulation of protein ubiquitination / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / replication fork / DNA methylation / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / PRC2 methylates histones and DNA / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Defective pyroptosis / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling
Similarity search - Function
Arc Repressor Mutant, subunit A - #2230 / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain ...Arc Repressor Mutant, subunit A - #2230 / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type 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 / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Arc Repressor Mutant, subunit A / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Ubiquitin B / Polyubiquitin-B / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsQian, C.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council General Research Fund17160016 Hong Kong
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation.
Authors: Li, T. / Wang, L. / Du, Y. / Xie, S. / Yang, X. / Lian, F. / Zhou, Z. / Qian, C.
History
DepositionSep 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B
B: DNA (cytosine-5)-methyltransferase 1
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2396
Polymers44,9843
Non-polymers2553
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-24 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.760, 131.760, 61.025
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Polyubiquitin-B


Mass: 8514.757 Da / Num. of mol.: 2 / Fragment: UNP residues 1-73
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS
#2: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / CXXC-type zinc finger protein 9 / DNA methyltransferase HsaI / M.HsaI / MCMT


Mass: 27954.336 Da / Num. of mol.: 1 / Fragment: RFTS domain, UNP residues 351-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT1, AIM, CXXC9, DNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P26358, DNA (cytosine-5-)-methyltransferase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#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.: 235 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8 / Details: 20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 79146 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 5.7
Reflection shellHighest resolution: 2.0032 Å / Rmerge(I) obs: 0.478

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Processing

Software
NameVersionClassification
PHENIXdev_2067refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV4

3av4


Resolution: 2.003→44.769 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.18
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2325 3874 4.9 %
Rwork0.1985 --
obs0.2001 79112 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.54 Å2 / Biso mean: 44.0152 Å2 / Biso min: 16.82 Å2
Refinement stepCycle: final / Resolution: 2.003→44.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 11 235 3335
Biso mean--108.82 39.43 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093165
X-RAY DIFFRACTIONf_angle_d1.4154296
X-RAY DIFFRACTIONf_chiral_restr0.062487
X-RAY DIFFRACTIONf_plane_restr0.01562
X-RAY DIFFRACTIONf_dihedral_angle_d10.4713064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0032-2.02760.32931520.25492636278897
2.0276-2.05320.29551430.25522662280599
2.0532-2.08030.27541100.237227052815100
2.0803-2.10880.23631380.22842666280497
2.1088-2.13890.22571710.221326672838100
2.1389-2.17080.26491010.21842688278998
2.1708-2.20470.261360.20892669280599
2.2047-2.24090.22681440.224726832827100
2.2409-2.27950.25711760.21942621279798
2.2795-2.3210.26061680.217726112779100
2.321-2.36560.28911100.2272736284698
2.3656-2.41390.25081440.218627132857100
2.4139-2.46640.3014840.22732714279899
2.4664-2.52370.26411580.227327002858100
2.5237-2.58680.25921180.22862719283799
2.5868-2.65680.23991520.2152637278999
2.6568-2.73490.23641360.223127202856100
2.7349-2.82320.23211370.22852682281999
2.8232-2.92410.25931660.229626662832100
2.9241-3.04110.25861800.229726872867100
3.0411-3.17950.27161290.229327042833100
3.1795-3.34710.2311440.212226852829100
3.3471-3.55670.26221240.201127272851100
3.5567-3.83120.2111340.18322703283799
3.8312-4.21650.26281450.161926812826100
4.2165-4.8260.15881440.14427142858100
4.826-6.07790.20981420.175927182860100
6.0779-44.78040.1525880.1692724281299

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