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- PDB-9dem: USP7 in complex with macrocycle MC04 -

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Basic information

Entry
Database: PDB / ID: 9dem
TitleUSP7 in complex with macrocycle MC04
Components
  • Macrocycle peptide MC04
  • 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: 1.77 Å
AuthorsRouge, L. / Ultsch, M. / 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
G: Macrocycle peptide MC04


Theoretical massNumber of molelcules
Total (without water)44,2952
Polymers44,2952
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-6 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.474, 67.709, 71.617
Angle α, β, γ (deg.)90.00, 125.22, 90.00
Int Tables number5
Space group name H-MC121

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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.: 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: Protein/peptide Macrocycle peptide MC04


Mass: 1818.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% v/v 2-Propanol, 0.1M Tris pH 8.0 and 5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.77→58.51 Å / Num. obs: 28314 / % possible obs: 65.9 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.061 / Rrim(I) all: 0.115 / Net I/σ(I): 6.6
Reflection shellResolution: 1.77→1.945 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1416 / CC1/2: 0.565 / Rpim(I) all: 0.515 / Rrim(I) all: 0.974 / % possible all: 13.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→35.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 2009 7.1 %
Rwork0.187 --
obs0.1905 28307 65.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 163 2969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152867
X-RAY DIFFRACTIONf_angle_d2.253861
X-RAY DIFFRACTIONf_dihedral_angle_d21.448382
X-RAY DIFFRACTIONf_chiral_restr0.091410
X-RAY DIFFRACTIONf_plane_restr0.013501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.291840.223956X-RAY DIFFRACTION2
1.82-1.870.2969140.2681170X-RAY DIFFRACTION6
1.87-1.920.3165540.2924687X-RAY DIFFRACTION24
1.92-1.980.2941920.27221227X-RAY DIFFRACTION43
1.99-2.060.32531130.26351547X-RAY DIFFRACTION55
2.06-2.140.25661430.25281764X-RAY DIFFRACTION63
2.14-2.240.3171440.24152019X-RAY DIFFRACTION71
2.24-2.350.25551770.22472240X-RAY DIFFRACTION79
2.35-2.50.26281860.24192478X-RAY DIFFRACTION88
2.5-2.690.29792180.24532771X-RAY DIFFRACTION97
2.69-2.960.28892180.21822837X-RAY DIFFRACTION99
2.96-3.390.2442190.19462839X-RAY DIFFRACTION99
3.39-4.270.21222130.1472829X-RAY DIFFRACTION98
4.27-35.730.1842140.1492834X-RAY DIFFRACTION97

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