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- PDB-7xhk: High-resolution X-ray cocrystal structure of USP7 in complex with... -

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Basic information

Entry
Database: PDB / ID: 7xhk
TitleHigh-resolution X-ray cocrystal structure of USP7 in complex with LX04-46
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 / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / 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 / DNA alkylation repair / regulation of DNA-binding transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / 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 / 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 / protein ubiquitination / 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-DVU / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 LX04-46
Authors: Wen, X.A.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 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
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8562
Polymers40,2681
Non-polymers5871
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15460 Å2
Unit cell
Length a, b, c (Å)75.961, 70.856, 77.584
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-726-

HOH

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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: 40268.445 Da / Num. of mol.: 1
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-DVU / ~{N}-[[4-[6-[[1-[[2-chloranyl-4-(furan-2-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-3-yl]phenyl]methyl]methanamide


Mass: 587.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H31ClN6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20mg/ml Crystal, 100mM Tris,20% PEG 1000, PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→12.87 Å / Num. obs: 17003 / % possible obs: 99.4 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.32
Reflection shellResolution: 2.3→12.87 Å / Rmerge(I) obs: 0.093 / Num. unique obs: 17003

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M1K

6m1k


Resolution: 2.3→12.87 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 791 4.65 %
Rwork0.2203 16212 -
obs0.2223 17003 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.64 Å2 / Biso mean: 62.1903 Å2 / Biso min: 36.47 Å2
Refinement stepCycle: final / Resolution: 2.3→12.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 42 47 2674
Biso mean--53.81 55.1 -
Num. residues----334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.440.33781010.32612734283595
2.44-2.630.33761430.32272571271489
2.63-2.890.38581360.3112528266488
2.89-3.30.31541430.26522625276891
3.3-4.140.26321330.20482837297098
4.14-12.870.19541350.172917305299
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)
13.80330.70890.16752.50650.9763.3111-0.13460.9249-0.7029-0.14070.18670.01020.35990.0075-0.03150.3787-0.06320.02020.4948-0.14090.4067-40.4931-8.326119.8501
25.5973-2.1532-1.46282.31990.32060.4287-0.21840.2860.04590.3390.2913-0.73230.23810.27620.00270.5283-0.0476-0.05390.6135-0.16050.6729-11.9739-0.44120.9839
36.17521.0454-0.18523.74820.29271.6705-0.23251.30870.5773-0.28280.29250.1176-0.1773-0.1576-0.09890.3783-0.0296-0.0220.60390.10540.3501-36.15336.200117.7685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 211 through 325 )B211 - 325
2X-RAY DIFFRACTION2chain 'B' and (resid 326 through 420 )B326 - 420
3X-RAY DIFFRACTION3chain 'B' and (resid 421 through 553 )B421 - 553

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