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- PDB-4z97: Crystal structure of USP7 in complex with DNMT1(K1115Q) -

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Basic information

Entry
Database: PDB / ID: 4z97
TitleCrystal structure of USP7 in complex with DNMT1(K1115Q)
Components
  • DNA (cytosine-5)-methyltransferase 1
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / complex / TRANSFERASE
Function / homology
Function and homology information


negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / regulation of telomere capping / : / : / 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 / : / : / 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. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type 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 / Resolution: 2.998 Å
AuthorsZhang, Z.M. / Song, J.
CitationJournal: To Be Published
Title: Crystal structure of USP7 in complex with DNMT1(K1115Q)
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 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4363
Polymers65,3442
Non-polymers921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-1 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.659, 123.659, 152.928
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: 3456.802 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*PLUS, DNA (cytosine-5-)-methyltransferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 5.17 Å3/Da / Density % sol: 76.19 %
Crystal growTemperature: 297 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: 2.998→43.861 Å / Num. obs: 27615 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementResolution: 2.998→43.861 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 2016 7.3 %
Rwork0.2089 --
obs0.2121 27611 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.998→43.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 6 0 4094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084221
X-RAY DIFFRACTIONf_angle_d1.1545719
X-RAY DIFFRACTIONf_dihedral_angle_d14.821531
X-RAY DIFFRACTIONf_chiral_restr0.044628
X-RAY DIFFRACTIONf_plane_restr0.005755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.998-3.07260.41041370.33271790X-RAY DIFFRACTION100
3.0726-3.15570.32381420.31771801X-RAY DIFFRACTION100
3.1557-3.24850.36781420.27831830X-RAY DIFFRACTION100
3.2485-3.35330.31911420.26031791X-RAY DIFFRACTION100
3.3533-3.47310.28271400.25231814X-RAY DIFFRACTION100
3.4731-3.61210.28551400.23291805X-RAY DIFFRACTION100
3.6121-3.77650.25981460.21711815X-RAY DIFFRACTION100
3.7765-3.97540.27091420.20881825X-RAY DIFFRACTION100
3.9754-4.22430.23011430.19791799X-RAY DIFFRACTION100
4.2243-4.55020.2131460.16491826X-RAY DIFFRACTION100
4.5502-5.00750.19681480.15461837X-RAY DIFFRACTION100
5.0075-5.73070.26071460.1861849X-RAY DIFFRACTION100
5.7307-7.21490.25841490.24251858X-RAY DIFFRACTION100
7.2149-43.86550.24221530.19941955X-RAY DIFFRACTION100
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)
11.588-0.76461.75332.9944-0.48042.3888-0.02370.2354-0.49560.14840.4621-0.01130.07830.1356-0.46520.6866-0.10470.24060.8287-0.19440.6368-60.2038-33.4089-2.5777
20.81160.1446-0.64344.72871.31831.67680.1911-0.1860.2137-0.52630.2178-0.5031-0.35010.4182-0.34180.7129-0.1616-0.04820.6575-0.190.7151-36.808426.105120.7742
35.9307-2.1282-2.13542.07121.53363.2146-0.2465-0.0067-0.3487-0.27480.134-0.86030.18630.17060.11440.9938-0.17350.4320.61220.14360.7684-64.0763-36.817811.1483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 555 through 800 )
2X-RAY DIFFRACTION2chain 'A' and (resid 801 through 1083 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1110 through 1117 )

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