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- PDB-4yoc: Crystal Structure of human DNMT1 and USP7/HAUSP complex -

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Basic information

Entry
Database: PDB / ID: 4yoc
TitleCrystal Structure of human DNMT1 and USP7/HAUSP complex
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsTRANSFERASE/HYDROLASE / DNA methylation / Deubiquitination / DNA methyltransferase / Modification / TRANSFERASE-HYDROLASE complex
Function / homology
Function and homology information


negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / regulation of telomere capping / : / positive regulation of DNA demethylation / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi ...negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / regulation of telomere capping / : / positive regulation of DNA demethylation / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / SUMOylation of DNA methylation proteins / negative regulation of gene expression via chromosomal CpG island methylation / 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 / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / pericentric heterochromatin / negative regulation of TORC1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA methylation / replication fork / PRC2 methylates histones and DNA / regulation of signal transduction by p53 class mediator / Defective pyroptosis / promoter-specific chromatin binding / cellular response to amino acid stimulus / regulation of protein stability / NoRC negatively regulates rRNA expression / regulation of circadian rhythm / 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 / rhythmic process / Regulation of TP53 Degradation / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / negative regulation of gene expression / DNA-templated transcription / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / DNA binding / RNA 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. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / DNA methylase, C-5 cytosine-specific, conserved site ...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. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / 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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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. / Papain-like cysteine peptidase superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
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 / molecular replacement / Resolution: 2.916 Å
AuthorsCheng, J. / Yang, H. / Fang, J. / Gong, R. / Wang, P. / Li, Z. / Xu, Y.
CitationJournal: Nat Commun / Year: 2015
Title: Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.
Authors: Cheng, J. / Yang, H. / Fang, J. / Ma, L. / Gong, R. / Wang, P. / Li, Z. / Xu, Y.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 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_initial_refinement_model / pdbx_struct_oper_list
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_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: DNA (cytosine-5)-methyltransferase 1
C: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,1544
Polymers178,0232
Non-polymers1312
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.231, 111.619, 163.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / CXXC-type zinc finger protein 9 / DNA methyltransferase HsaI / M.HsaI / MCMT


Mass: 113916.836 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 600-1600
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
#2: 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: 64106.008 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 560-1102
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 6-8% PEG 3350, 200 mM potassium acetate / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2013
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 44471 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 61.62 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.063 / Net I/av σ(I): 19.087 / Net I/σ(I): 8.1 / Num. measured all: 615406
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-313.50.85843671.141100
3-3.1213.60.61943951.14100
3.12-3.2713.60.4443821.11299.9
3.27-3.4413.70.30343921.085100
3.44-3.6513.80.21744011.061100
3.65-3.9413.90.17544161.022100
3.94-4.3314.20.14944411.033100
4.33-4.9614.30.13244620.982100
4.96-6.2413.80.10345161.09199.9
6.24-50140.05346990.98399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SWR, 2YLM

3swr

2ylm


Resolution: 2.916→49.419 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1991 4.48 %
Rwork0.2077 42405 -
obs0.21 44396 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.41 Å2 / Biso mean: 66.1918 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 2.916→49.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11368 0 2 11 11381
Biso mean--67.8 42.54 -
Num. residues----1411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311649
X-RAY DIFFRACTIONf_angle_d0.89215743
X-RAY DIFFRACTIONf_chiral_restr0.0351662
X-RAY DIFFRACTIONf_plane_restr0.0042066
X-RAY DIFFRACTIONf_dihedral_angle_d14.84420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9162-2.98910.41481240.28992689281389
2.9891-3.06990.37391440.277229953139100
3.0699-3.16020.33111460.26630153161100
3.1602-3.26220.34181390.252830043143100
3.2622-3.37880.27261480.240930103158100
3.3788-3.5140.2731410.226630133154100
3.514-3.67390.29411460.223430523198100
3.6739-3.86750.25481410.214830153156100
3.8675-4.10980.25521420.196730643206100
4.1098-4.42690.2181430.176230393182100
4.4269-4.8720.17681400.16130633203100
4.872-5.57620.22411390.179930853224100
5.5762-7.02220.25671430.210331213264100
7.0222-49.42620.25361550.20093240339599

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