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- PDB-9del: USP7 in complex with macrocycle MC03 -

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Basic information

Entry
Database: PDB / ID: 9del
TitleUSP7 in complex with macrocycle MC03
Components
  • Macrocycle peptide MC03
  • 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
Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
D: Macrocycle peptide MC03
C: Macrocycle peptide MC03


Theoretical massNumber of molelcules
Total (without water)88,4784
Polymers88,4784
Non-polymers00
Water25214
1
A: Ubiquitin carboxyl-terminal hydrolase 7
C: Macrocycle peptide MC03


Theoretical massNumber of molelcules
Total (without water)44,2392
Polymers44,2392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-10 kcal/mol
Surface area15450 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
D: Macrocycle peptide MC03


Theoretical massNumber of molelcules
Total (without water)44,2392
Polymers44,2392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-10 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.913, 69.417, 76.408
Angle α, β, γ (deg.)90.00, 91.93, 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 MC03


Mass: 1761.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 25 %w/v PEG 1500, 0.1 M MMT pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.397→74.871 Å / Num. obs: 20952 / % possible obs: 75.62 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.039 / Net I/σ(I): 15.2
Reflection shellResolution: 2.397→2.586 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1049 / CC1/2: 0.639 / Rpim(I) all: 0.639 / Rrim(I) all: 0.905 / % possible all: 45.69

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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: 2.5→42.81 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2721 1054 5.1 %
Rwork0.2164 --
obs0.2189 20664 75.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5549 0 0 14 5563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025673
X-RAY DIFFRACTIONf_angle_d0.4527675
X-RAY DIFFRACTIONf_dihedral_angle_d13.912087
X-RAY DIFFRACTIONf_chiral_restr0.038820
X-RAY DIFFRACTIONf_plane_restr0.0031004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.36871030.32771604X-RAY DIFFRACTION51
2.61-2.750.36451210.32482085X-RAY DIFFRACTION65
2.75-2.920.38821920.3252747X-RAY DIFFRACTION86
2.92-3.150.33231560.28642740X-RAY DIFFRACTION85
3.15-3.470.31261180.27812727X-RAY DIFFRACTION84
3.47-3.970.23691060.21822459X-RAY DIFFRACTION75
3.97-50.20811430.17362674X-RAY DIFFRACTION82
5-42.810.28611150.18232574X-RAY DIFFRACTION77
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)
15.064-0.2647-0.0523.5516-0.69871.8260.103-0.28780.0256-0.312-0.13790.11050.15070.1610.00030.8398-0.0121-0.0190.76390.05050.5929-27.670713.74140.3696
23.72411.41260.26424.71890.91351.56620.1155-0.0749-0.07370.012-0.0627-0.1388-0.0023-0.18670.00490.6709-0.0073-0.01620.62610.09980.5923-11.365812.034838.4169
30.04950.02820.03520.03960.03840.03920.2293-0.1828-0.36570.8383-0.1248-0.86880.75640.60470.00030.9769-0.1649-0.13890.90520.1180.89750.396212.248450.8434
40.0739-0.03350.04480.0354-0.05330.07810.01870.4847-0.4009-0.8920.32741.07840.6049-0.9512-0.00011.11780.0936-0.17911.0945-0.00171.0736-40.058112.8338-11.2336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 212 through 552)
2X-RAY DIFFRACTION2(chain 'B' and resid 211 through 553)
3X-RAY DIFFRACTION3(chain 'D' and resid 0 through 14)
4X-RAY DIFFRACTION4(chain 'C' and resid 0 through 14)

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