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- PDB-9vvv: Crystal structure of USP15 catalytic domain in complex with Ub-PA -

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Basic information

Entry
Database: PDB / ID: 9vvv
TitleCrystal structure of USP15 catalytic domain in complex with Ub-PA
Components
  • Polyubiquitin-C
  • Ubiquitin carboxyl-terminal hydrolase 15
KeywordsLYASE / DUB / Cysteine protease / Complex
Function / homology
Function and homology information


negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / regulation of RNA metabolic process / monoubiquitinated protein deubiquitination / ubiquitin-modified histone reader activity / deubiquitinase activity / transforming growth factor beta receptor binding / transcription elongation-coupled chromatin remodeling ...negative regulation of antifungal innate immune response / regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / regulation of RNA metabolic process / monoubiquitinated protein deubiquitination / ubiquitin-modified histone reader activity / deubiquitinase activity / transforming growth factor beta receptor binding / transcription elongation-coupled chromatin remodeling / K48-linked deubiquitinase activity / SMAD binding / BMP signaling pathway / protein deubiquitination / transforming growth factor beta receptor signaling pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Asymmetric localization of PCP proteins / negative regulation of transforming growth factor beta receptor signaling pathway / Fanconi Anemia Pathway / Ubiquitin-dependent degradation of Cyclin D / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Deactivation of the beta-catenin transactivating complex / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Stabilization of p53 / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Assembly of the pre-replicative complex / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis / Vpu mediated degradation of CD4
Similarity search - Function
Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : ...Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsLiu, B. / Xu, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201026 China
National Science Foundation (NSF, China)Q23C050003 China
CitationJournal: Commun Biol / Year: 2026
Title: Structural insights into ubiquitin recognition by USP15 revealed through a covalent activity-based probe.
Authors: Liu, B. / Wang, T. / Luo, H. / Lang, L. / Liu, X. / Gong, Z. / Wang, T. / Cheng, W. / Xie, L. / Zhang, X. / Fang, X. / Xu, X.
History
DepositionJul 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 15
C: Polyubiquitin-C
B: Ubiquitin carboxyl-terminal hydrolase 15
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4357
Polymers96,2354
Non-polymers2003
Water2,684149
1
A: Ubiquitin carboxyl-terminal hydrolase 15
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2524
Polymers48,1182
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-7 kcal/mol
Surface area16880 Å2
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 15
D: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1833
Polymers48,1182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-10 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.873, 131.851, 139.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 15 / Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 ...Deubiquitinating enzyme 15 / Ubiquitin thioesterase 15 / Ubiquitin-specific-processing protease 15 / Unph-2 / Unph4


Mass: 39558.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues from P469 to F785 are deleted and a linker containing residues ASTSK are inserted.
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-C


Mass: 8558.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The ubiquitin molecule, specifically its first 75 amino acids, is conjugated with a PA group at the 75th glycine residue (75G), forming a unique linkage.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 50% MPD, 0.1M Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.304→77.35 Å / Num. obs: 53563 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.99 Å2 / CC1/2: 0.995 / CC star: 0.973 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Net I/σ(I): 9.6
Reflection shellResolution: 2.304→2.386 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 5204 / CC1/2: 0.538 / CC star: 0.74 / Rpim(I) all: 0.512 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
PHASERphasing
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→38.677 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 2658 4.98 %
Rwork0.2217 --
obs0.2242 53365 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.304→38.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 7 149 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156719
X-RAY DIFFRACTIONf_angle_d1.4439071
X-RAY DIFFRACTIONf_dihedral_angle_d7.8614050
X-RAY DIFFRACTIONf_chiral_restr0.063983
X-RAY DIFFRACTIONf_plane_restr0.011175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.34590.36381240.31652594X-RAY DIFFRACTION98
2.3459-2.3910.37651230.29932632X-RAY DIFFRACTION99
2.391-2.43980.311370.29612643X-RAY DIFFRACTION99
2.4398-2.49290.34771360.28952627X-RAY DIFFRACTION99
2.4929-2.55080.34911550.29092617X-RAY DIFFRACTION100
2.5508-2.61460.39051190.28242678X-RAY DIFFRACTION100
2.6146-2.68530.34681660.2862634X-RAY DIFFRACTION100
2.6853-2.76430.31821640.27032614X-RAY DIFFRACTION99
2.7643-2.85350.32981640.26362653X-RAY DIFFRACTION100
2.8535-2.95540.3141200.24852667X-RAY DIFFRACTION100
2.9554-3.07370.29051580.25332639X-RAY DIFFRACTION100
3.0737-3.21360.3161390.24482696X-RAY DIFFRACTION100
3.2136-3.38290.26191540.23142649X-RAY DIFFRACTION100
3.3829-3.59470.2711420.22232687X-RAY DIFFRACTION100
3.5947-3.8720.27341270.2172710X-RAY DIFFRACTION100
3.872-4.26120.25541640.19362663X-RAY DIFFRACTION100
4.2612-4.87680.19781150.16772717X-RAY DIFFRACTION100
4.8768-6.14030.23651100.19652759X-RAY DIFFRACTION100
6.1403-8.5040.23791410.19882828X-RAY DIFFRACTION99

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