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- PDB-5vsb: Structure of DUB complex -

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Basic information

Entry
Database: PDB / ID: 5vsb
TitleStructure of DUB complex
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHydrolase/Inhibitor / deubiquitinase / inhibitor / protein-inhibitor complex / Hydrolase-Inhibitor 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 / negative regulation of NF-kappaB transcription factor activity ...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 / 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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 ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-9QA / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7.
Authors: Lamberto, I. / Liu, X. / Seo, H.S. / Schauer, N.J. / Iacob, R.E. / Hu, W. / Das, D. / Mikhailova, T. / Weisberg, E.L. / Engen, J.R. / Anderson, K.C. / Chauhan, D. / Dhe-Paganon, S. / Buhrlage, S.J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8604
Polymers82,0092
Non-polymers8522
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.970, 73.740, 84.770
Angle α, β, γ (deg.)90.000, 91.430, 90.000
Int Tables number4
Space group name H-MP1211

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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: 41004.340 Da / Num. of mol.: 2 / Fragment: UNP residues 192-544
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
#2: Chemical ChemComp-9QA / 7-chloro-3-{[4-hydroxy-1-(3-phenylpropanoyl)piperidin-4-yl]methyl}quinazolin-4(3H)-one


Mass: 425.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24ClN3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, NaFormate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.15
ReflectionResolution: 1.85→61.95 Å / Num. obs: 64979 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.93.21.225199.3
8.27-73.743.30.046198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→61.951 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.23
RfactorNum. reflection% reflection
Rfree0.2494 3226 4.96 %
Rwork0.2346 --
obs0.2353 64976 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.98 Å2 / Biso mean: 38.6858 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: final / Resolution: 1.85→61.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 108 353 5751
Biso mean--33.72 41.91 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015470
X-RAY DIFFRACTIONf_angle_d0.4627400
X-RAY DIFFRACTIONf_chiral_restr0.038798
X-RAY DIFFRACTIONf_plane_restr0.002956
X-RAY DIFFRACTIONf_dihedral_angle_d16.1093266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8506-1.88250.36331520.3893053320594
1.8825-1.91670.36681610.36383022318394
1.9167-1.95350.36621280.34383119324796
1.9535-1.99340.32531550.31833092324795
1.9934-2.03670.35651390.31283080321995
2.0367-2.08410.31411980.29833058325694
2.0841-2.13620.2821670.28873060322795
2.1362-2.1940.28211420.29173093323595
2.194-2.25850.28571420.27513096323896
2.2585-2.33140.26321610.28183067322895
2.3314-2.41460.30441460.28523133327995
2.4146-2.51130.29361550.28043062321795
2.5113-2.62550.28671560.27423118327495
2.6255-2.76380.26391630.25613077324095
2.7638-2.93680.25831420.25743131327395
2.9368-3.16330.24421580.23123079323795
3.1633-3.48120.23361830.2113073325694
3.4812-3.98390.21431620.18433094325695
3.9839-5.01520.19961950.16483078327393
5.0152-29.33340.23311680.19973155332394
Refinement TLS params.Method: refined / Origin x: 124.3662 Å / Origin y: -3.9607 Å / Origin z: 106.464 Å
111213212223313233
T0.1814 Å20.0258 Å2-0.0002 Å2-0.1247 Å2-0.0145 Å2--0.1506 Å2
L0.3492 °20.0389 °20.0148 °2-0.305 °2-0.041 °2--0.2681 °2
S-0.0053 Å °0.0409 Å °0.0245 Å °-0.0196 Å °-0.0106 Å °-0.0096 Å °0.0404 Å °0.0161 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA211 - 554
2X-RAY DIFFRACTION1allA4000
3X-RAY DIFFRACTION1allB208 - 548
4X-RAY DIFFRACTION1allB4000
5X-RAY DIFFRACTION1allS1 - 353

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