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- PDB-3pv1: Crystal structure of the USP15 DUSP-UBL domains -

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Basic information

Entry
Database: PDB / ID: 3pv1
TitleCrystal structure of the USP15 DUSP-UBL domains
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination / transcription elongation-coupled chromatin remodeling / BMP signaling pathway / SMAD binding / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DUSP-like / DUSP-like / 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 ...DUSP-like / DUSP-like / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsElliott, P.R. / Urbe, S. / Clague, M.J. / Barsukov, I.L.
CitationJournal: Febs Lett. / Year: 2011
Title: Structural variability of the ubiquitin specific protease DUSP-UBL double domains.
Authors: Elliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9723
Polymers51,9132
Non-polymers591
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area24980 Å2
MethodPISA
2
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9436
Polymers103,8254
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10260 Å2
ΔGint-72 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.660, 122.980, 105.050
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 thiolesterase 15 / Ubiquitin-specific-processing protease 15 ...Deubiquitinating enzyme 15 / Ubiquitin thiolesterase 15 / Ubiquitin-specific-processing protease 15 / Unph-2 / Unph4


Mass: 25956.283 Da / Num. of mol.: 2 / Fragment: DUSP-UBL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 18% PEG 4000, 0.1M Tris, 0.1M magnesium acetate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2009
RadiationMonochromator: double crystal 28.290m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→53.07 Å / Num. all: 19545 / Num. obs: 19389 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.740.741.7199.9
2.74-53.070.0993.7196.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.938 Å / SU ML: 0.41 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.274 991 5.13 %Random
Rwork0.2049 ---
obs0.2085 19336 98.62 %-
all-19341 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.396 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2011 Å20 Å20 Å2
2--4.3156 Å20 Å2
3----4.5167 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 4 92 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083610
X-RAY DIFFRACTIONf_angle_d1.0844881
X-RAY DIFFRACTIONf_dihedral_angle_d17.6871340
X-RAY DIFFRACTIONf_chiral_restr0.066523
X-RAY DIFFRACTIONf_plane_restr0.005621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73710.32681370.26922615X-RAY DIFFRACTION100
2.7371-2.90850.29911400.23682621X-RAY DIFFRACTION100
2.9085-3.1330.27771400.20762602X-RAY DIFFRACTION99
3.133-3.44810.30411560.20332594X-RAY DIFFRACTION99
3.4481-3.94670.24411450.17772616X-RAY DIFFRACTION99
3.9467-4.97090.22311440.15092619X-RAY DIFFRACTION98
4.9709-39.94260.26631290.2052678X-RAY DIFFRACTION96
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)
12.07210.07480.52242.511-0.92231.635-0.03990.0027-0.9896-0.09660.1445-0.66630.18490.1410.00020.37080.00170.15190.2814-0.14460.585720.72528.5676-21.4665
23.95770.8555-0.17672.427-0.84892.0255-0.0803-0.37520.0940.09670.11470.06530.30820.2689-00.31230.09910.03530.27720.01730.1809-31.830431.5486-28.9869
31.2309-0.5564-0.75242.0475-0.46962.78690.1540.30810.2813-0.1360.1023-0.035-0.5903-0.682700.27460.02910.06720.3583-0.00290.2933-1.517438.0996-48.0815
43.0535-0.7033-1.13762.71182.29972.8735-0.1226-0.0524-0.00130.0673-0.08580.00510.19910.0066-0.00020.22130.0482-0.02030.16850.00720.2639-6.331714.18162.4474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 6:131
2X-RAY DIFFRACTION2chain A and resseq 132:223
3X-RAY DIFFRACTION3chain B and resseq 6:131
4X-RAY DIFFRACTION4chain B and resseq 132:223

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