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- PDB-3mqs: Crystal Structure of the USP7:Hdm2(PSTS) complex -

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Basic information

Entry
Database: PDB / ID: 3mqs
TitleCrystal Structure of the USP7:Hdm2(PSTS) complex
Components
  • Hdm2 peptide
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / deubiquitinase activity / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / deubiquitinase activity / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / DNA alkylation repair / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / peroxisome proliferator activated receptor binding / response to iron ion / negative regulation of protein processing / K48-linked deubiquitinase activity / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / symbiont-mediated disruption of host cell PML body / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / protein deubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / protein sumoylation / SUMOylation of transcription factors / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / transcription-coupled nucleotide-excision repair / protein autoubiquitination / cellular response to actinomycin D / negative regulation of gluconeogenesis / ribonucleoprotein complex binding / negative regulation of TORC1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / Regulation of PTEN localization / positive regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / regulation of signal transduction by p53 class mediator / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / Signaling by ALK fusions and activated point mutants / establishment of protein localization / regulation of protein stability / Oncogene Induced Senescence / regulation of circadian rhythm / Regulation of TP53 Activity through Methylation / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / cellular response to gamma radiation / Formation of TC-NER Pre-Incision Complex / response to toxic substance / cellular response to growth factor stimulus / PML body / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / Regulation of TP53 Degradation / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / negative regulation of neuron projection development / chromosome
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MATH/TRAF domain ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / 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. / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSaridakis, V.
CitationJournal: To be Published
Title: Crystal Structure of USP7
Authors: Sarkari, F. / La Delfa, A. / Arrowsmith, C.H. / Frappier, L. / Sheng, Y. / Saridakis, V.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Hdm2 peptide


Theoretical massNumber of molelcules
Total (without water)19,1892
Polymers19,1892
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-3 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 69.840, 45.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 18133.102 Da / Num. of mol.: 1 / Fragment: UNP residues 54-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAUSP, USP7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, EC: 3.1.2.15
#2: Protein/peptide Hdm2 peptide


Mass: 1056.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q00987*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2M Lithium Sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→25.8 Å / Num. obs: 8727 / Redundancy: 4.5 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.159 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 868 / Rsym value: 0.46

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YY6

1yy6


Resolution: 2.4→25.8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 233152.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 912 10.6 %RANDOM
Rwork0.214 ---
obs0.214 8581 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.083 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 102 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.162.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 163 11.9 %
Rwork0.272 1210 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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