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- PDB-9den: USP7 in complex with macrocycle MC07 -

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Basic information

Entry
Database: PDB / ID: 9den
TitleUSP7 in complex with macrocycle MC07
Components
  • Macrocycle peptide MC07
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / USP7 / HAUSP / macrocycle / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / 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 ...regulation of telomere capping / regulation of establishment of protein localization to telomere / 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 gluconeogenesis / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of circadian rhythm / regulation of protein stability / 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 / p53 binding / rhythmic process / Regulation of TP53 Degradation / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / nuclear body / 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 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
ETHANOL / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsUltsch, M. / Tenorio, C.A. / Dueber, E.C. / Harris, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Discovery and characterization of potent macrocycle inhibitors of ubiquitin-specific protease-7.
Authors: Miranda, R. / Anson, F. / Smith, S.T. / Ultsch, M. / Tenorio, C.A. / Rouge, L. / Farrell, B. / Adaligil, E. / Holden, J.K. / Harris, S.F. / Dueber, E.C.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: 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
B: Ubiquitin carboxyl-terminal hydrolase 7
A: Ubiquitin carboxyl-terminal hydrolase 7
D: Macrocycle peptide MC07
C: Macrocycle peptide MC07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7885
Polymers88,7424
Non-polymers461
Water1629
1
B: Ubiquitin carboxyl-terminal hydrolase 7
D: Macrocycle peptide MC07


Theoretical massNumber of molelcules
Total (without water)44,3712
Polymers44,3712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-5 kcal/mol
Surface area16820 Å2
MethodPISA
2
A: Ubiquitin carboxyl-terminal hydrolase 7
C: Macrocycle peptide MC07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4173
Polymers44,3712
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.362, 69.675, 77.617
Angle α, β, γ (deg.)90.00, 94.36, 90.00
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: 42476.953 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: Protein/peptide Macrocycle peptide MC07


Mass: 1894.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% w/v PEG 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.93→41.66 Å / Num. obs: 17031 / % possible obs: 97.05 % / Redundancy: 3.5 % / Biso Wilson estimate: 72.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Net I/σ(I): 11.71
Reflection shellResolution: 2.93→3.035 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1707 / CC1/2: 0.954 / Rpim(I) all: 0.26 / Rrim(I) all: 0.51 / % possible all: 97.92

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→41.66 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 878 5.19 %
Rwork0.2244 --
obs0.2258 16923 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.93→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5677 0 3 9 5689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045798
X-RAY DIFFRACTIONf_angle_d0.7047803
X-RAY DIFFRACTIONf_dihedral_angle_d12.5362182
X-RAY DIFFRACTIONf_chiral_restr0.045826
X-RAY DIFFRACTIONf_plane_restr0.0041016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.110.35571350.34122679X-RAY DIFFRACTION98
3.11-3.350.35331510.3282671X-RAY DIFFRACTION98
3.35-3.690.29661760.26972665X-RAY DIFFRACTION98
3.69-4.230.24111270.2382628X-RAY DIFFRACTION96
4.23-5.320.1991620.18352699X-RAY DIFFRACTION98
5.32-41.660.21891270.17732703X-RAY DIFFRACTION95
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)
12.6553-0.70370.1731.8739-0.36091.719-0.26-0.5593-0.7961-0.00770.2856-0.12750.14180.12570.00040.79770.01280.07990.99030.22080.94123.13582.9-1.7147
22.04581.2213-0.20190.18810.55490.11340.0052-0.0751-0.3923-0.249-0.07120.29810.1245-0.08430.0010.82710.0353-0.01531.1650.2950.9442-4.22347.01350.2683
33.73260.216-0.31252.3227-0.33111.0209-0.0124-0.3410.04980.1568-0.0449-0.0302-0.01210.1439-0.00160.7658-0.0007-0.00781.14260.1010.697316.089815.54121.9294
41.7362-0.44340.28881.1751-0.95870.6064-0.27530.32210.13110.18480.04260.2960.0131-0.5287-0.00330.7654-0.00180.02850.74280.18740.721511.67956.273538.3884
50.05060.06830.10340.10110.0335-0.0359-0.23380.3768-0.42290.428-0.15860.470.1537-0.1838-00.8354-0.0707-0.02930.7750.27910.9548.648-5.859936.3508
61.9518-0.6336-0.01151.32670.2671.3773-0.0589-0.1953-0.61190.07630.212-0.03830.15460.135-0.00170.76920.0161-0.05040.56940.13680.714229.58832.087139.4278
70.56530.3177-0.28932.54710.14250.2604-0.6433-0.41550.90380.55270.2631-0.7966-0.1313-0.13050.00840.87980.0109-0.04670.8322-0.08290.792351.97694.058139.6482
82.08890.0943-0.02442.38110.3781.9362-0.10970.00950.27320.14590.3778-0.0503-0.1401-0.3628-0.0020.76680.067-0.00910.64660.1560.664424.85515.482441.0067
93.4731-0.8344-0.8442.84591.6220.3578-0.1013-0.00770.3226-0.12040.13660.2806-0.0716-0.6820.00230.75570.0113-0.04690.69360.17550.776819.124914.988835.8044
100.23740.53360.1181.11560.38580.1331-1.09170.7142-1.6477-0.2066-0.35590.5186-0.1646-1.25290.06010.8971-0.0834-0.08061.0165-0.14711.4904-1.8963-7.669835.5521
110.01380.05770.13470.30310.30220.3435-0.4141-0.4818-0.849-0.8341-0.1256-0.10971.3242-0.673401.0542-0.16710.00791.0059-0.01720.98855.77566.9885-16.0587
120.31790.35560.18250.5173-0.02860.2115-0.76080.0345-0.18861.34640.0775-0.82860.1486-0.81570.00051.07970.23590.02510.85240.31040.860128.38054.705855.4024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 210 through 295 )
2X-RAY DIFFRACTION2chain 'B' and (resid 296 through 419 )
3X-RAY DIFFRACTION3chain 'B' and (resid 420 through 553 )
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 244 )
5X-RAY DIFFRACTION5chain 'A' and (resid 245 through 269 )
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 367 )
7X-RAY DIFFRACTION7chain 'A' and (resid 368 through 400 )
8X-RAY DIFFRACTION8chain 'A' and (resid 401 through 487 )
9X-RAY DIFFRACTION9chain 'A' and (resid 488 through 537 )
10X-RAY DIFFRACTION10chain 'A' and (resid 538 through 553 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 13 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 14 )

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