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- PDB-4z96: Crystal structure of DNMT1 in complex with USP7 -

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Basic information

Entry
Database: PDB / ID: 4z96
TitleCrystal structure of DNMT1 in complex with USP7
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / DNMT1
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 / regulation of telomere capping / regulation of establishment of protein localization to telomere / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi ...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 / regulation of telomere capping / regulation of establishment of protein localization to telomere / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA (cytosine-5-)-methyltransferase activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / deubiquitinase activity / SUMOylation of DNA methylation proteins / DNA alkylation repair / STAT3 nuclear events downstream of ALK signaling / female germ cell nucleus / methyl-CpG binding / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / lncRNA binding / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of gluconeogenesis / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA methylation / regulation of signal transduction by p53 class mediator / replication fork / PRC2 methylates histones and DNA / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / regulation of circadian rhythm / regulation of protein stability / NoRC negatively regulates rRNA expression / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / Regulation of TP53 Degradation / rhythmic process / chromosome / methylation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / negative regulation of gene expression / cysteine-type endopeptidase activity / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / proteolysis / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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. ...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. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhang, Z.M. / Song, J.
CitationJournal: To Be Published
Title: Crystal structure of DNMT1 in complex with USP7
Authors: Zhang, Z.M. / Song, J.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...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_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
C: DNA (cytosine-5)-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)65,3452
Polymers65,3452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint0 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.044, 124.044, 153.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 61887.328 Da / Num. of mol.: 1 / Fragment: UNP residues 544-1067
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / CXXC-type zinc finger protein 9 / DNA methyltransferase HsaI / M.HsaI / MCMT


Mass: 3457.853 Da / Num. of mol.: 1 / Fragment: UNP residues 1097-1129
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

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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: 5.2 Å3/Da / Density % sol: 76.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate, pH5.5, 10% PEG6000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 31086 / % possible obs: 94.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.6
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLM

2ylm


Resolution: 2.85→43.96 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1909 6.42 %
Rwork0.2008 --
obs0.2037 29741 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 0 0 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014221
X-RAY DIFFRACTIONf_angle_d1.3585722
X-RAY DIFFRACTIONf_dihedral_angle_d15.4871526
X-RAY DIFFRACTIONf_chiral_restr0.054630
X-RAY DIFFRACTIONf_plane_restr0.006754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.92130.39071290.34081875X-RAY DIFFRACTION89
2.9213-3.00030.33631290.31031916X-RAY DIFFRACTION90
3.0003-3.08850.3471350.29461956X-RAY DIFFRACTION92
3.0885-3.18820.28261390.26611967X-RAY DIFFRACTION92
3.1882-3.30210.28221330.24212011X-RAY DIFFRACTION94
3.3021-3.43430.29881390.25241999X-RAY DIFFRACTION94
3.4343-3.59050.29471410.2192026X-RAY DIFFRACTION95
3.5905-3.77970.24831350.21432008X-RAY DIFFRACTION94
3.7797-4.01630.23891400.19592017X-RAY DIFFRACTION93
4.0163-4.32620.22321370.17992012X-RAY DIFFRACTION94
4.3262-4.76110.19641410.1512042X-RAY DIFFRACTION94
4.7611-5.44890.18021360.16072061X-RAY DIFFRACTION94
5.4489-6.86090.25741400.20542072X-RAY DIFFRACTION94
6.8609-43.96570.25781350.19441870X-RAY DIFFRACTION82
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)
14.4851.53452.22552.78161.61982.92470.2278-0.1286-0.3694-0.34170.2092-0.3474-0.17490.0922-0.41670.8340.04560.27820.50270.11850.601-2.8054-72.7443-30.372
25.9591-5.3256-2.69485.90442.00011.13180.155-0.11710.4912-0.38170.0813-0.2887-0.2124-0.0974-0.19480.72640.02870.06920.7208-0.14670.5629-13.6486-42.3489-16.7222
32.66480.8919-1.61343.47750.23262.84140.82610.16611.13980.0655-0.02980.2933-0.9382-0.2701-0.56071.05510.23870.32150.5838-0.02970.9337-52.3941-9.22571.5534
47.38461.07441.82897.5459-1.19922.00570.11410.10310.89250.8932-0.5064-0.0895-0.51360.08170.19740.64360.14490.08690.64290.39830.4792-0.2515-73.6539-13.9921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 555 through 745 )
2X-RAY DIFFRACTION2chain 'A' and (resid 746 through 904 )
3X-RAY DIFFRACTION3chain 'A' and (resid 905 through 1083 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1108 through 1115 )

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