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- PDB-5vsk: Structure of DUB complex -

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Basic information

Entry
Database: PDB / ID: 5vsk
TitleStructure of DUB complex
ComponentsUbiquitin carboxyl-terminal hydrolase 7
Keywordshydrolase/hydrolase inhibitor / deubiquitinase / inhibitor / protein-inhibitor complex / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / 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 ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / 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 / 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 / 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 / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / 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-9HS / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.33 Å
AuthorsSeo, H.-Y. / 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

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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)83,1508
Polymers82,0092
Non-polymers1,1426
Water181
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5754
Polymers41,0041
Non-polymers5713
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5754
Polymers41,0041
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.390, 69.630, 77.970
Angle α, β, γ (deg.)90.000, 99.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 208 through 213 or (resid 214...
21(chain B and (resid 208 through 276 or (resid 277...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 208 through 213 or (resid 214...A208 - 213
121(chain A and (resid 208 through 213 or (resid 214...A214
131(chain A and (resid 208 through 213 or (resid 214...A208 - 552
141(chain A and (resid 208 through 213 or (resid 214...A208 - 552
151(chain A and (resid 208 through 213 or (resid 214...A208 - 552
161(chain A and (resid 208 through 213 or (resid 214...A208 - 552
211(chain B and (resid 208 through 276 or (resid 277...B208 - 276
221(chain B and (resid 208 through 276 or (resid 277...B277 - 278
231(chain B and (resid 208 through 276 or (resid 277...B208 - 551
241(chain B and (resid 208 through 276 or (resid 277...B208 - 551
251(chain B and (resid 208 through 276 or (resid 277...B208 - 551
261(chain B and (resid 208 through 276 or (resid 277...B208 - 551

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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
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-9HS / 7-chloro-3-({4-hydroxy-1-[(3S)-3-phenylbutanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one


Mass: 439.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26ClN3O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.37 Å3/Da / Density % sol: 48 % / Mosaicity: 0.18 °
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 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.33→48.65 Å / Num. obs: 11226 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 120.7 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Net I/σ(I): 13.6 / Num. measured all: 37783
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRpim(I) allRrim(I) allDiffraction-ID% possible all
3.33-3.393.21.60.550.997198
9.02-48.663.135.30.0180.033198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→44.154 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.35
RfactorNum. reflection% reflection
Rfree0.2736 576 5.14 %
Rwork0.2183 --
obs0.2211 11213 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 279.32 Å2 / Biso mean: 121.9359 Å2 / Biso min: 61.35 Å2
Refinement stepCycle: final / Resolution: 3.33→44.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 118 1 4682
Biso mean--155.43 118.39 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024731
X-RAY DIFFRACTIONf_angle_d0.4826477
X-RAY DIFFRACTIONf_chiral_restr0.039746
X-RAY DIFFRACTIONf_plane_restr0.002843
X-RAY DIFFRACTIONf_dihedral_angle_d11.7872735
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2269X-RAY DIFFRACTION11.261TORSIONAL
12B2269X-RAY DIFFRACTION11.261TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.33-3.6650.33151290.27812643277299
3.665-4.1950.31771590.25352629278898
4.195-5.28380.2531510.19612656280799
5.2838-44.15750.25851370.2082709284698
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)
18.4054-0.63060.65455.7287-1.68877.4447-0.439-0.21950.7854-0.44840.0536-0.0706-0.2926-0.00920.40450.53130.0534-0.00970.6199-0.16870.845157.0527-50.1277188.682
28.56671.60330.75621.98180.68620.22630.0687-0.20560.2807-0.1634-0.2167-0.271-0.09270.31730.17410.79560.0755-0.041.0226-0.01011.018380.9483-60.783193.1162
35.8109-3.59110.60424.79190.41122.2272-0.0589-0.039-0.1816-0.0253-0.11370.60730.0708-0.10930.28680.6678-0.1623-0.03890.8643-0.04360.876755.9218-62.6421189.9428
47.07590.65341.03282.1579-3.00979.42370.1172-0.23720.52720.205-0.3976-0.3649-0.79650.9660.23750.86760.02310.0260.73370.02280.787451.7926-49.8068227.4911
56.6651-1.1256-0.47671.68322.92425.28260.2491-0.07450.0609-0.62090.06671.052-0.59-1.6419-0.22121.0472-0.0944-0.23471.13090.19720.904131.758-63.0623222.6808
68.9004-1.0015-0.76814.1432-0.89696.30760.0725-0.29-0.8056-0.0039-0.0930.74550.4957-1.2242-0.50361.3831-0.2343-0.40021.23220.18251.268436.2076-66.9405228.7057
75.07720.5497-5.00262.85190.17775.12670.2668-1.7031-0.8312-0.86540.6302-0.41390.74520.8098-0.53341.1789-0.0546-0.2491.5085-0.0230.887547.0322-65.1506232.7927
82.60191.9228-1.88598.94371.29893.69630.50190.2665-2.07690.4053-0.1543-1.23241.73361.95560.07581.13940.2815-0.19561.60320.06331.273554.026-68.2172231.0926
94.8461-0.52620.42654.84760.69294.27440.36420.31790.2053-1.2274-0.6889-0.6027-0.98471.29560.20091.2572-0.3320.33011.0407-0.05440.749458.4253-51.5858219.5507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 208 through 325 )A208 - 325
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 464 )A326 - 464
3X-RAY DIFFRACTION3chain 'A' and (resid 465 through 552 )A465 - 552
4X-RAY DIFFRACTION4chain 'B' and (resid 208 through 331 )B208 - 331
5X-RAY DIFFRACTION5chain 'B' and (resid 332 through 407 )B332 - 407
6X-RAY DIFFRACTION6chain 'B' and (resid 408 through 446 )B408 - 446
7X-RAY DIFFRACTION7chain 'B' and (resid 447 through 464 )B447 - 464
8X-RAY DIFFRACTION8chain 'B' and (resid 465 through 514 )B465 - 514
9X-RAY DIFFRACTION9chain 'B' and (resid 515 through 551 )B515 - 551

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