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- PDB-9dep: USP7 in complex with macrocycle MC09 -

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Basic information

Entry
Database: PDB / ID: 9dep
TitleUSP7 in complex with macrocycle MC09
Components
  • Macrocycle peptide MC09
  • 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: 2.57 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
C: Macrocycle peptide MC09
D: Macrocycle peptide MC09
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Macrocycle peptide MC09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0817
Polymers132,9856
Non-polymers961
Water30617
1
A: Ubiquitin carboxyl-terminal hydrolase 7
C: Macrocycle peptide MC09


Theoretical massNumber of molelcules
Total (without water)44,3282
Polymers44,3282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-10 kcal/mol
Surface area15830 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
D: Macrocycle peptide MC09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4243
Polymers44,3282
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-29 kcal/mol
Surface area16560 Å2
MethodPISA
3
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Macrocycle peptide MC09


Theoretical massNumber of molelcules
Total (without water)44,3282
Polymers44,3282
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.997, 68.848, 76.052
Angle α, β, γ (deg.)90.000, 105.210, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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.: 3
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 MC09


Mass: 1851.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 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: 2.57→73.39 Å / Num. obs: 27109 / % possible obs: 69.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 68.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.04 / Rrim(I) all: 0.058 / Net I/σ(I): 9.7
Reflection shellResolution: 2.572→2.664 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1355 / CC1/2: 0.582 / CC star: 0.631 / Rpim(I) all: 0.61 / Rrim(I) all: 0.869 / % possible all: 5.32

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→73.39 Å / SU ML: 0.3651 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.4232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 1370 5.06 %
Rwork0.2469 25731 -
obs0.2488 27101 69.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.74 Å2
Refinement stepCycle: LAST / Resolution: 2.57→73.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 5 17 8006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288158
X-RAY DIFFRACTIONf_angle_d0.57911095
X-RAY DIFFRACTIONf_chiral_restr0.04071234
X-RAY DIFFRACTIONf_plane_restr0.00411468
X-RAY DIFFRACTIONf_dihedral_angle_d16.37042868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.660.440580.397198X-RAY DIFFRACTION5.33
2.66-2.770.3806470.3594872X-RAY DIFFRACTION23.48
2.77-2.90.36351290.34041939X-RAY DIFFRACTION53.45
2.9-3.050.36171880.34113283X-RAY DIFFRACTION89.67
3.05-3.240.36041710.33243709X-RAY DIFFRACTION99.54
3.24-3.380.37121050.3172172X-RAY DIFFRACTION98.79
3.5-3.840.33321550.28153121X-RAY DIFFRACTION84.67
3.84-4.40.29561440.23573004X-RAY DIFFRACTION80.45
4.4-5.540.23771860.20093730X-RAY DIFFRACTION99.49
5.54-73.390.24072370.20873703X-RAY DIFFRACTION97.4
Refinement TLS params.Method: refined / Origin x: -39.7509621993 Å / Origin y: 17.2841918509 Å / Origin z: 16.8985922852 Å
111213212223313233
T0.297159142092 Å20.0891077359849 Å2-0.108953894544 Å2-0.382145995954 Å2-0.0963321216575 Å2--0.239434916596 Å2
L0.960199516293 °20.322721296141 °2-0.574937776898 °2-1.52386144326 °2-0.121900709566 °2--0.621190897206 °2
S-0.080825725117 Å °0.0935532641258 Å °-0.0416373531878 Å °0.0489351282094 Å °0.163784171805 Å °-0.393437519111 Å °-0.0541508862893 Å °-0.0960421621638 Å °-0.0858352447849 Å °
Refinement TLS groupSelection details: all

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