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- PDB-2fop: The Crystal Structure of the N-terminal domain of HAUSP/USP7 comp... -

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Basic information

Entry
Database: PDB / ID: 2fop
TitleThe Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with mdm2 peptide 147-150
Components
  • Ubiquitin carboxyl-terminal hydrolase 7
  • mdm2 peptide
KeywordsHYDROLASE / MATH Domain
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / cellular response to vitamin B1 / response to formaldehyde / monoubiquitinated protein deubiquitination / response to water-immersion restraint stress / cellular response to UV-C / response to ether / regulation of retrograde transport, endosome to Golgi / fibroblast activation ...regulation of telomere capping / regulation of establishment of protein localization to telomere / cellular response to vitamin B1 / response to formaldehyde / monoubiquitinated protein deubiquitination / response to water-immersion restraint stress / cellular response to UV-C / response to ether / regulation of retrograde transport, endosome to Golgi / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Trafficking of AMPA receptors / DNA alkylation repair / deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / receptor serine/threonine kinase binding / cellular response to alkaloid / K48-linked deubiquitinase activity / response to steroid hormone / SUMO transferase activity / regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of protein processing / peroxisome proliferator activated receptor binding / positive regulation of vascular associated smooth muscle cell migration / AKT phosphorylates targets in the cytosol / response to iron ion / NEDD8 ligase activity / symbiont-mediated disruption of host cell PML body / regulation of protein catabolic process / positive regulation of muscle cell differentiation / cellular response to peptide hormone stimulus / cellular response to antibiotic / regulation of postsynaptic neurotransmitter receptor internalization / SUMOylation of ubiquitinylation proteins / negative regulation of gene expression via chromosomal CpG island methylation / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / negative regulation of signal transduction by p53 class mediator / cellular response to estrogen stimulus / negative regulation of gluconeogenesis / protein localization to nucleus / protein sumoylation / response to magnesium ion / ribonucleoprotein complex binding / protein deubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / protein autoubiquitination / positive regulation of mitotic cell cycle / NPAS4 regulates expression of target genes / positive regulation of protein export from nucleus / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / DNA damage response, signal transduction by p53 class mediator / : / regulation of signal transduction by p53 class mediator / Regulation of PTEN localization / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / response to cocaine / negative regulation of neuron projection development / establishment of protein localization / cellular response to gamma radiation / ubiquitin binding / regulation of protein stability / Stabilization of p53 / protein destabilization / Regulation of RUNX3 expression and activity / cellular response to growth factor stimulus / PML body / response to toxic substance / RING-type E3 ubiquitin transferase / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / Degradation of CDH1 / cellular response to hydrogen peroxide / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / disordered domain specific binding / p53 binding / ubiquitin-protein transferase activity / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / endocytic vesicle membrane / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin protein ligase activity / rhythmic process / chromosome / protein-containing complex assembly / 5S rRNA binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation
Similarity search - Function
MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass ...MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / p53 negative regulator Mdm2/Mdm4 / TRAF-like / 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 superfamily / Zinc finger RanBP2-type signature. / 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 C-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaridakis, V. / Sheng, Y. / Sarkari, F. / Duan, S. / Wu, T. / Arrowsmith, C.H. / Frappier, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Molecular recognition of p53 and MDM2 by USP7/HAUSP
Authors: Sheng, Y. / Saridakis, V. / Sarkari, F. / Duan, S. / Wu, T. / Arrowsmith, C.H. / Frappier, L.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: mdm2 peptide


Theoretical massNumber of molelcules
Total (without water)18,7682
Polymers18,7682
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.900, 69.900, 45.700
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 thiolesterase 7 / Ubiquitin-specific processing protease 7 / Deubiquitinating enzyme 7 / ...Ubiquitin thiolesterase 7 / Ubiquitin-specific processing protease 7 / Deubiquitinating enzyme 7 / Herpesvirus associated ubiquitin-specific protease


Mass: 18133.102 Da / Num. of mol.: 1 / Fragment: MATH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAUSP, USP7 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, EC: 3.1.2.15
#2: Protein/peptide mdm2 peptide


Mass: 634.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q00987*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4K, 0.1 M Tris, 0.2 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 13054 / Num. obs: 10923 / Redundancy: 2.5 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.112 / Net I/σ(I): 4.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.543

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YY6

1yy6


Resolution: 2.1→19.9 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 170841.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 549 5 %RANDOM
Rwork0.206 ---
obs0.206 10915 83.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0416 Å2 / ksol: 0.371217 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2---1.19 Å20 Å2
3---2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 138 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 67 4.1 %
Rwork0.243 1580 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.top
X-RAY DIFFRACTION3water_rep.param

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