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- PDB-5c56: Crystal structure of USP7/HAUSP in complex with ICP0 -

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Basic information

Entry
Database: PDB / ID: 5c56
TitleCrystal structure of USP7/HAUSP in complex with ICP0
Components
  • Ubiquitin E3 ligase ICP0
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / virus protein ICP0 / USP7 / deubiquitination
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / release from viral latency / regulation of telomere capping / suppression by virus of host type I interferon production / monoubiquitinated protein deubiquitination / viral tegument / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / response to type I interferon ...symbiont-mediated perturbation of host exit from mitosis / release from viral latency / regulation of telomere capping / suppression by virus of host type I interferon production / monoubiquitinated protein deubiquitination / viral tegument / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / response to type I interferon / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / ligase activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / RING-type E3 ubiquitin transferase / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / Regulation of TP53 Degradation / p53 binding / chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / host cell nucleus / protein-containing complex / proteolysis / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...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 / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin E3 ligase ICP0 / E3 ubiquitin-protein ligase ICP0 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.685 Å
AuthorsCheng, J. / Li, Z. / Gong, R. / Fang, J. / Yang, Y. / Sun, C. / Yang, H. / Xu, Y.
CitationJournal: Protein Cell / Year: 2015
Title: Molecular mechanism for the substrate recognition of USP7.
Authors: Cheng, J. / Li, Z. / Gong, R. / Fang, J. / Yang, Y. / Sun, C. / Yang, H. / Xu, Y.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 8, 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
B: Ubiquitin E3 ligase ICP0
A: Ubiquitin carboxyl-terminal hydrolase 7


Theoretical massNumber of molelcules
Total (without water)66,3372
Polymers66,3372
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-4 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.879, 80.378, 151.149
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/peptide Ubiquitin E3 ligase ICP0


Mass: 2230.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 606-626 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1)
References: UniProt: D3YPC2, UniProt: P08393*PLUS
#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) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.79 Å3/Da / Density % sol: 67.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Sodium Bromide / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.685→50 Å / Num. obs: 27389 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 69.25 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Χ2: 1.037 / Net I/av σ(I): 16.74 / Net I/σ(I): 10.6 / Num. measured all: 166411
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.685-2.86.20.86626790.7820.3740.9451.01100
2.8-2.916.20.57227170.8910.2480.6251.062100
2.91-3.046.20.40526830.9450.1750.4421.057100
3.04-3.26.20.26627130.9730.1150.2911.053100
3.2-3.46.20.17927060.9840.0780.1951.053100
3.4-3.666.10.12627350.990.0540.1370.991100
3.66-4.036.10.09927370.9930.0430.1081.023100
4.03-4.626.10.09527480.9930.0410.1031.07199.8
4.62-5.815.90.08127760.9930.0350.0890.98699.7
5.81-505.60.04528950.9960.0210.051.0698.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLM

2ylm


Resolution: 2.685→42.46 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 2002 7.33 %
Rwork0.2155 25328 -
obs0.219 27330 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.96 Å2 / Biso mean: 76.2301 Å2 / Biso min: 32.47 Å2
Refinement stepCycle: final / Resolution: 2.685→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 0 6 4446
Biso mean---53.38 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014541
X-RAY DIFFRACTIONf_angle_d1.4786126
X-RAY DIFFRACTIONf_chiral_restr0.064651
X-RAY DIFFRACTIONf_plane_restr0.007806
X-RAY DIFFRACTIONf_dihedral_angle_d17.1621748
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 (%)
2.685-2.75210.41381260.35751655178193
2.7521-2.82650.39081510.309317831934100
2.8265-2.90970.29961360.27417971933100
2.9097-3.00360.34171440.269217881932100
3.0036-3.11090.32851440.2517961940100
3.1109-3.23540.31291450.242317951940100
3.2354-3.38260.27431410.254518091950100
3.3826-3.56080.28251440.240118191963100
3.5608-3.78380.30531390.224918151954100
3.7838-4.07570.28531430.213718141957100
4.0757-4.48550.23361460.193618431989100
4.4855-5.13360.20881450.174518171962100
5.1336-6.46410.26281480.199518662014100
6.4641-42.46580.21331500.19271931208198

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