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- PDB-4ysi: Structure of USP7 with a novel viral protein -

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Basic information

Entry
Database: PDB / ID: 4ysi
TitleStructure of USP7 with a novel viral protein
Components
  • SER-PRO-GLY-GLU-GLY-PRO-SER-GLY
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/Peptide / USP7 / viral protein / HYDROLASE-Peptide complex
Function / homology
Function and homology information


regulation of telomere capping / positive regulation of DNA demethylation / : / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body ...regulation of telomere capping / positive regulation of DNA demethylation / : / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / 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 / protein sequestering activity / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / protein stabilization / nuclear body / protein ubiquitination / transcription cis-regulatory region binding / Ub-specific processing proteases / DNA-binding transcription factor activity / protein domain specific binding / cysteine-type endopeptidase activity / host cell nucleus / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding 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 ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding 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 / SMAD-like domain superfamily / 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. / SMAD/FHA domain superfamily / Papain-like cysteine peptidase superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
VIRF-1 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.02 Å
AuthorsChavoshi, S. / Saridakis, V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106583 Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of USP7 with a novel viral protein
Authors: Chavoshi, S. / Egorova, O. / Lacdao, I.K. / Farhadi, S. / Sheng, Y. / Saridakis, V.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: SER-PRO-GLY-GLU-GLY-PRO-SER-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5943
Polymers17,5022
Non-polymers921
Water4,810267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-1 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.975, 69.975, 45.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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: 16814.838 Da / Num. of mol.: 1 / Fragment: UNP residues 63-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide SER-PRO-GLY-GLU-GLY-PRO-SER-GLY


Mass: 686.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 8 / References: UniProt: F5HF68*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG4K, 0.2M LiSO4, 0.1M TrisHCl / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.02→49.48 Å / Num. obs: 111563 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Net I/σ(I): 20.6 / Num. measured all: 684942
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.02-1.15.50.5313125204228210.8880.24699.3
2.7-49.486.50.03157.24055461920.9990.01399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimless0.3.8data scaling
PHASERphasing
RESOLVEphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YY6

1yy6


Resolution: 1.02→31.294 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.16 2000 1.79 %Random
Rwork0.1539 109526 --
obs0.1541 111526 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.18 Å2 / Biso mean: 18.6359 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.02→31.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 14 267 1474
Biso mean--18.51 32.31 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061236
X-RAY DIFFRACTIONf_angle_d0.9091671
X-RAY DIFFRACTIONf_chiral_restr0.093167
X-RAY DIFFRACTIONf_plane_restr0.006216
X-RAY DIFFRACTIONf_dihedral_angle_d19.44436
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 (%)
1.0198-1.04530.24031420.26037710785299
1.0453-1.07360.22711420.22427787792999
1.0736-1.10520.1931410.195977267867100
1.1052-1.14080.18231410.174878247965100
1.1408-1.18160.1631430.164877887931100
1.1816-1.22890.17521410.165378217962100
1.2289-1.28490.16551450.164877957940100
1.2849-1.35260.15811420.1678117953100
1.3526-1.43730.17591440.158378407984100
1.4373-1.54830.17151450.149778417986100
1.5483-1.70410.14191440.144778457989100
1.7041-1.95070.14451390.141178467985100
1.9507-2.45750.1371430.144978648007100
2.4575-31.30850.16471480.148580288176100
Refinement TLS params.Method: refined / Origin x: 29.4682 Å / Origin y: -9.5957 Å / Origin z: -18.5993 Å
111213212223313233
T0.0706 Å2-0.0048 Å20.0031 Å2-0.0673 Å20.0139 Å2--0.0509 Å2
L0.877 °20.6309 °20.5138 °2-2.2692 °21.2232 °2--1.4479 °2
S0.0287 Å °-0.0459 Å °-0.047 Å °0.0673 Å °-0.0282 Å °0.026 Å °0.038 Å °-0.0365 Å °-0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA63 - 205
2X-RAY DIFFRACTION1allB44 - 51
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1 - 268

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