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- PDB-7xhh: High-resolution X-ray cocrystal structure of USP7 in complex with X4 -

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Basic information

Entry
Database: PDB / ID: 7xhh
TitleHigh-resolution X-ray cocrystal structure of USP7 in complex with X4
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Inhibitor / USP7 / Complex
Function / homology
Function and homology information


regulation of telomere capping / : / 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 / : / 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
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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-DYO / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSun, H.B. / Wen, X.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773584, 91853125 China
CitationJournal: To Be Published
Title: High-resolution X-ray cocrystal structure of USP7 in complex with X4
Authors: Wen, X.A.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)81,6454
Polymers80,5232
Non-polymers1,1222
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area32360 Å2
Unit cell
Length a, b, c (Å)76.034, 68.904, 81.788
Angle α, β, γ (deg.)90.000, 100.320, 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: 40261.492 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) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-DYO / 3-[4-(aminomethyl)phenyl]-6-[[1-[[2-chloranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-pyrazolo[4,3-d]pyrimidin-7-one


Mass: 561.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29ClN8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris (hydroxymethyl)aminomethane hydrochloride, pH 7.0, 20% (v/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48351 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 52.65 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Χ2: 1.012 / Net I/σ(I): 5.2 / Num. measured all: 295466
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.30.72822250.7760.3470.810.4291.6
2.14-2.184.70.64123280.7860.3030.7120.43996.6
2.18-2.225.10.57524090.8780.2670.6360.45999.6
2.22-2.265.30.50723950.890.2370.5610.47299.9
2.26-2.315.80.44324340.9170.1980.4870.475100
2.31-2.376.40.40524180.9440.1720.4410.496100
2.37-2.426.60.35523990.9480.1480.3850.53100
2.42-2.496.60.28724340.9720.120.3110.562100
2.49-2.566.50.25324220.9750.1060.2750.609100
2.56-2.656.40.21724300.9750.0920.2370.698100
2.65-2.746.10.18824400.9780.0830.2060.803100
2.74-2.856.20.16524120.9840.0720.180.901100
2.85-2.986.70.14324150.9870.0590.1551.038100
2.98-3.146.70.12924510.9870.0540.141.321100
3.14-3.336.60.1124140.9910.0460.121.517100
3.33-3.596.20.09824320.990.0430.1071.873100
3.59-3.956.50.08624530.9930.0370.0941.972100
3.95-4.526.80.07424540.9950.0310.081.904100
4.52-5.76.30.06424650.9960.0280.071.654100
5.7-506.50.0525210.9980.0220.0551.21599.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M1K

6m1k


Resolution: 2.1→34.45 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.08 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2181 1992 4.2 %
Rwork0.196 45492 -
obs0.197 47484 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.74 Å2 / Biso mean: 66.5183 Å2 / Biso min: 36.87 Å2
Refinement stepCycle: final / Resolution: 2.1→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 138 136 5846
Biso mean--61.3 60.01 -
Num. residues----686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.35681200.31912822294284
2.15-2.210.29471400.27873074321494
2.21-2.270.27471400.24453208334897
2.27-2.350.27481440.23653219336397
2.35-2.430.25481430.23743235337897
2.43-2.530.30071340.22933278341298
2.53-2.640.32591620.23813260342299
2.64-2.780.24811270.23273318344599
2.78-2.960.28241520.24123308346099
2.96-3.190.27131440.23423307345199
3.19-3.510.261530.219933463499100
3.51-4.010.2061490.193633443493100
4.01-5.050.18021460.153833883534100
5.05-34.450.15161380.15863385352398
Refinement TLS params.Method: refined / Origin x: 15.4057 Å / Origin y: -0.9311 Å / Origin z: 20.3068 Å
111213212223313233
T0.3415 Å2-0.0113 Å2-0.0317 Å2-0.367 Å2-0.0163 Å2--0.3571 Å2
L0.4714 °20.0656 °2-0.1851 °2-0.5169 °2-0.1351 °2--0.1503 °2
S-0.0183 Å °0.054 Å °-0.0635 Å °0.0142 Å °-0.0256 Å °0.0302 Å °0.016 Å °0.0075 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA207 - 553
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allB208 - 553
4X-RAY DIFFRACTION1allB601
5X-RAY DIFFRACTION1allS1 - 136

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