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- PDB-4wph: Crystal structure of USP7 ubiquitin-like domains in compact confo... -

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Basic information

Entry
Database: PDB / ID: 4wph
TitleCrystal structure of USP7 ubiquitin-like domains in compact 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 / positive regulation of DNA demethylation / suppression by virus of host type I interferon production / monoubiquitinated protein deubiquitination / viral tegument / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation ...symbiont-mediated perturbation of host exit from mitosis / release from viral latency / regulation of telomere capping / positive regulation of DNA demethylation / suppression by virus of host type I interferon production / monoubiquitinated protein deubiquitination / viral tegument / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / 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 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 / regulation of protein stability / RING-type E3 ubiquitin transferase / regulation of circadian rhythm / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / rhythmic process / ubiquitin protein ligase activity / 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 / cysteine-type deubiquitinase activity / host cell cytoplasm / protein stabilization / protein ubiquitination / nuclear body / Ub-specific processing proteases / 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 / Resolution: 2.92 Å
AuthorsPfoh, R. / Lacdao, I. / Saridakis, V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106583 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
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
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_oper_list.symmetry_operation
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.number_atoms_total / _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)90,4508
Polymers90,3084
Non-polymers1424
Water70339
1
A: Ubiquitin carboxyl-terminal hydrolase 7
D: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2605
Polymers45,1542
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-19 kcal/mol
Surface area20490 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
C: ICP0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1903
Polymers45,1542
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.336, 92.336, 190.283
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
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: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 543 - 880 / Label seq-ID: 30 - 367

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: 43838.535 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.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3000, sodium citrate, L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.92→30.6 Å / Num. obs: 21012 / % possible obs: 99.5 % / Redundancy: 1.86 % / Net I/σ(I): 22.19
Reflection shellResolution: 2.92→3.02 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.92→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.2153 / FOM work R set: 0.8089 / SU B: 39.065 / SU ML: 0.319 / SU R Cruickshank DPI: 0.373 / SU Rfree: 0.4123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 1039 5 %RANDOM
Rwork0.2328 19939 --
obs0.2342 19939 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 209.61 Å2 / Biso mean: 76.499 Å2 / Biso min: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.41 Å20 Å2
2---0.41 Å20 Å2
3---1.34 Å2
Refinement stepCycle: final / Resolution: 2.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5519 0 4 39 5562
Biso mean--84.19 48.5 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195653
X-RAY DIFFRACTIONr_bond_other_d0.0030.025376
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9717627
X-RAY DIFFRACTIONr_angle_other_deg0.856312372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08624.371286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.954151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091542
X-RAY DIFFRACTIONr_chiral_restr0.0670.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216362
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021300
Refine LS restraints NCS

Ens-ID: 1 / Number: 18948 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.92→2.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 70 -
Rwork0.424 1447 -
all-1517 -
obs--99.87 %
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)
10.04750.06920.0990.79030.0650.5052-0.0271-0.04610.0203-0.1228-0.0411-0.1482-0.04550.08870.06820.29990.22240.10790.31260.04830.089325.726-0.392-25.229
20.60130.06380.17120.3621-0.0930.08620.1261-0.098-0.0311-0.0489-0.1196-0.00850.03510.0032-0.00640.42920.2990.10010.35130.11110.03821.898-26.118-8.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A540 - 2120
2X-RAY DIFFRACTION1D618 - 626
3X-RAY DIFFRACTION2B543 - 2117
4X-RAY DIFFRACTION2C617 - 626

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