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- PDB-4wpi: Crystal structure of USP7 ubiquitin-like domains in extended conf... -

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Basic information

Entry
Database: PDB / ID: 4wpi
TitleCrystal structure of USP7 ubiquitin-like domains in extended conformation
Components
  • ICP0
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / deubiquitinating (DUB) enzyme / ubiquitin-like (Ubl) domains / ICP0 binding site / HAUSP
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 / negative regulation of gene expression via chromosomal CpG island methylation / 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 / 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 / Regulation of TP53 Degradation / rhythmic process / 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 / cysteine-type deubiquitinase activity / host cell cytoplasm / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / host cell nucleus / protein-containing complex / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ICP0 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Herpes simplex virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsPfoh, R. / Lacdao, I.K.L. / Saridakis, V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106853 Canada
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structure of USP7 Ubiquitin-like Domains with an ICP0 Peptide Reveals a Novel Mechanism Used by Viral and Cellular Proteins to Target USP7.
Authors: Pfoh, R. / Lacdao, I.K. / Georges, A.A. / Capar, A. / Zheng, H. / Frappier, L. / Saridakis, V.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Ubiquitin carboxyl-terminal hydrolase 7
C: ICP0
D: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7287
Polymers91,6214
Non-polymers1063
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 7
D: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8824
Polymers45,8112
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15 kcal/mol
Surface area20540 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
C: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8463
Polymers45,8112
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-17 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.990, 164.990, 110.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 543 - 881 / Label seq-ID: 30 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 44495.059 Da / Num. of mol.: 2 / Fragment: ubiquitin-like domain (UNP residues 535-888)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: p15tv-l / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)mgk / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide ICP0


Mass: 1315.594 Da / Num. of mol.: 2 / Fragment: USP7 binding sequence / Source method: obtained synthetically / Source: (synth.) Herpes simplex virus (type 1 / strain 17) / References: UniProt: P08393*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium chloride, TRIS-HCl, 2-mercaptoethanol, betaine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97849 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 3.4→42.3 Å / Num. obs: 21462 / % possible obs: 99.7 % / Redundancy: 9.5 % / Net I/σ(I): 24.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.3133 / WRfactor Rwork: 0.2443 / FOM work R set: 0.7639 / SU B: 75.906 / SU ML: 0.496 / SU R Cruickshank DPI: 0.5115 / SU Rfree: 0.5178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 1138 5.3 %RANDOM
Rwork0.2409 20318 --
obs0.2429 20318 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 384.52 Å2 / Biso mean: 187.526 Å2 / Biso min: 94.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2--3.51 Å20 Å2
3----7.01 Å2
Refinement stepCycle: final / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5724 0 3 0 5727
Biso mean--150.21 --
Num. residues----701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195841
X-RAY DIFFRACTIONr_bond_other_d0.0030.025559
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9847878
X-RAY DIFFRACTIONr_angle_other_deg0.874312823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.40924.658307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.785151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8441543
X-RAY DIFFRACTIONr_chiral_restr0.0660.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216607
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021344
Refine LS restraints NCS

Ens-ID: 1 / Number: 19856 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.4→3.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 91 -
Rwork0.429 1463 -
all-1554 -
obs--99.55 %
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)
10.97120.42010.42210.42790.12750.50040.26990.3434-0.01480.5910.03090.0708-0.22890.0228-0.30081.17120.0880.34230.21420.08250.20962.13219.78518.393
20.22260.0766-0.24180.6308-1.02141.734-0.07670.0993-0.1875-0.1461-0.1981-0.13430.34320.32350.27470.4443-0.051-0.29610.5090.02750.576176.49424.62614.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A540 - 885
2X-RAY DIFFRACTION1D617 - 626
3X-RAY DIFFRACTION2B543 - 881
4X-RAY DIFFRACTION2C617 - 626

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