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- PDB-3lmn: Oligomeric structure of the DUSP domain of human USP15 -

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Basic information

Entry
Database: PDB / ID: 3lmn
TitleOligomeric structure of the DUSP domain of human USP15
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE / UCH / USP / DUB / DEUBIQUITYLATION / DEUBIQUITINATING ENZYME / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / UBIQUITIN CARBOXYTERMINAL HYDROLASE / CLEAVAGE / USP15 / DUB15 / UBP15 / ENDOPEPTIDASE / THIOLESTERASE / DUSP / DOMAIN-SWAPPING / STRUCTURAL GENOMICS CONSORTIUM (SGC) / Acetylation / Alternative splicing / Phosphoprotein / Protease / Thiol protease / Ubl conjugation pathway
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 / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity ...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 / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / SMAD binding / protein deubiquitination / BMP signaling pathway / 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 / Ub-specific processing proteases / nuclear body / 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. / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWalker, J.R. / Asinas, A. / Avvakumov, G.V. / Alenkin, D. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human Ubiquitin-Specific Protease 15 DUSP Domain
Authors: Walker, J.R. / Asinas, A. / Avvakumov, G.V. / Alenkin, D. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionJan 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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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)31,1634
Polymers31,0572
Non-polymers1062
Water3,675204
1
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

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)124,65316
Polymers124,2288
Non-polymers4248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area25000 Å2
ΔGint-139 kcal/mol
Surface area49840 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)62,3268
Polymers62,1144
Non-polymers2124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area10460 Å2
ΔGint-62 kcal/mol
Surface area26960 Å2
MethodPISA
3
A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1634
Polymers31,0572
Non-polymers1062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area2950 Å2
ΔGint-21 kcal/mol
Surface area15760 Å2
MethodPISA
4
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1774
Polymers31,0572
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.174, 138.174, 132.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 15528.555 Da / Num. of mol.: 2 / Fragment: DUSP DOMAIN, RESIDUES 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0529, USP15 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q9Y4E8, EC: 3.1.2.15
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 4.75 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: Crystals of the dusp domain of usp15 were grown at 291.1 K using the sitting drop method by mixing equal volumes of protein solution (15 mg/ml) and crystallization buffer (2.0 M ammonium ...Details: Crystals of the dusp domain of usp15 were grown at 291.1 K using the sitting drop method by mixing equal volumes of protein solution (15 mg/ml) and crystallization buffer (2.0 M ammonium formate, 0.1 M sodium acetate, pH 3.8.) The crystals were cryoprotected by immersion in well solution supplemented with 20% (v/v) glycerol prior to dunking and storage in liquid nitrogen., VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 7, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 35029 / Num. obs: 35029 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Rsym value: 0.083 / Net I/σ(I): 35.89
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 1727 / Rsym value: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JYU

3jyu


Resolution: 2.15→19.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.484 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20401 1749 5 %RANDOM
Rwork0.18337 ---
obs0.18442 33132 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.241 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 7 204 2327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222222
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9533014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14824.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.241159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211699
X-RAY DIFFRACTIONr_mcbond_it0.5551.51321
X-RAY DIFFRACTIONr_mcangle_it1.0422121
X-RAY DIFFRACTIONr_scbond_it1.8773901
X-RAY DIFFRACTIONr_scangle_it2.8484.5893
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 130 -
Rwork0.211 2376 -
obs--100 %
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)
15.72182.249-2.72914.1915-0.52679.4919-0.0984-0.2162-0.5342-0.0479-0.1389-0.14860.79870.16930.23730.12070.02440.05510.08470.00360.112640.40224.356132.489
28.4054-0.7941-1.70983.1734-0.95196.4784-0.09520.304-0.2261-0.41910.0044-0.23260.43990.08550.09080.17670.01620.04740.1538-0.03140.09245.791210.744714.6568
32.8755-0.64070.45720.1466-0.22086.68290.00570.2111-0.0108-0.0109-0.04510.0145-0.0562-0.1370.03940.1688-0.01490.00780.1865-0.00630.17337.598916.071721.3187
46.9334-2.60832.0035.2419-5.62776.1579-0.1036-0.40730.45990.2129-0.0861-0.2097-0.21870.14040.18970.1263-0.01410.02050.204-0.05130.144137.28316.631835.6646
56.5817-2.78655.63412.9157-2.04195.2237-0.06910.01460.3329-0.0679-0.1023-0.3556-0.15430.26740.17130.1193-0.00920.06670.29180.00190.184544.22210.128441.1391
69.46193.69535.0451.60050.98898.8354-0.23140.04140.109-0.11750.09150.0230.0734-0.43950.140.12460.00980.04290.25910.02260.154940.181910.258546.5114
71.86380.6013-0.65693.9754-5.43278.6612-0.0707-0.02960.0690.3106-0.1248-0.0493-0.5555-0.3650.19550.13010.01940.03690.2438-0.0530.180630.601417.594535.371
818.60886.2831.369123.8769-0.09447.3956-0.42660.07881.8313-0.35030.12872.7571-1.1437-1.28220.29790.38030.1999-0.08810.53120.04130.782325.15129.522522.3557
920.13034.0141-0.360110.56120.32253.8097-0.38850.61060.9712-0.2076-0.19470.1228-0.8031-0.42740.58320.3170.0546-0.05970.2360.04520.250936.387130.890422.9978
1011.58433.36320.778916.30712.572113.1037-0.05720.310.0088-0.1543-0.1266-0.4264-0.11290.63180.18390.104-0.0063-0.00680.10870.01680.142243.083624.326427.383
113.5551.6214-0.51472.543-1.03755.6726-0.10750.1016-0.2845-0.1016-0.09060.0780.2802-0.23110.19810.0925-0.01840.01310.1176-0.0280.088133.281210.354926.7664
1214.8526-0.3168-8.59932.6281-2.148412.38530.09030.8695-0.0974-0.24-0.00050.4527-0.1109-1.2535-0.08980.08760.0049-0.05010.2515-0.01080.135929.014418.969821.1648
1318.35517.8599-2.25235.5294-1.65941.40780.21270.29790.9186-0.2801-0.16680.2389-0.1846-0.0007-0.04580.2440.03650.0320.21230.0590.179548.410821.094210.4596
145.1627-4.421-1.20793.78991.03260.28930.26460.19240.5923-0.1923-0.162-0.4874-0.0966-0.0235-0.10260.39890.03180.00050.27160.09610.399468.849621.13019.7098
1511.1614-3.14591.87133.8378-0.771112.9393-0.0697-0.28660.1390.17740.03190.1959-0.0877-0.03320.03780.21230.05560.06440.09530.0170.093353.21117.164420.0902
163.5732-4.04110.430810.49391.52371.674-0.0971-0.1874-0.30730.53830.17060.10660.00390.0036-0.07350.18680.01960.05950.09970.02990.108561.0855-3.097720.1128
175.3574-0.42421.177111.3322-4.15958.3384-0.02540.0444-0.81020.1603-0.04310.11510.1680.1110.06850.06560.02160.01840.0606-0.0930.293359.6627-13.525712.9612
183.1806-4.4524-0.807213.07927.53337.79890.11180.41270.3212-0.4950.038-0.3375-0.56910.3868-0.14980.2639-0.03720.01680.26670.00260.188560.64950.7895.9222
197.15693.52643.53433.54350.83013.7573-0.06820.4237-0.0084-0.0820.158-0.22470.09770.1281-0.08980.20740.02410.04440.13060.01420.107562.18446.484112.1197
2012.018-4.66764.17015.3983-2.27382.42870.05140.41950.1258-0.0141-0.0699-0.2868-0.00810.07320.01850.21420.02060.02990.10810.02610.050362.627813.317412.0162
212.0131-1.49211.02169.30051.68541.29720.14520.337-0.2085-0.72170.00870.0399-0.11480.1238-0.15390.33490.0073-0.00750.3693-0.02250.191155.21922.20843.6337
2225.83293.7143-10.4643.68255.382720.953-1.0513.2833-0.7476-0.49350.3460.39021.0535-1.3740.7051.31350.1179-0.43920.9916-0.39910.71453.9117-12.0055-6.5351
2317.83255.485.868615.52736.910918.13080.49461.2193-0.6511-0.6223-0.0501-0.45580.69120.8113-0.44450.30880.10940.05440.2591-0.1380.145466.5764-11.03290.2253
246.9345-1.609-1.61654.50130.21334.02370.09660.0457-0.61060.01850.06520.3210.02220.1444-0.16180.0909-0.02260.01110.04-0.0680.18858.5226-8.184711.8502
254.8146-1.29852.03679.97775.35199.08520.0160.3397-0.2616-0.4978-0.02460.6573-0.3199-0.4340.00860.1165-0.03120.00340.1593-0.02560.210449.6456-1.91338.7239
268.4684-8.59839.652512.3307-9.952411.04910.331-0.0961-0.5756-0.31390.19090.88220.413-0.1691-0.52190.2839-0.02870.01810.2357-0.14560.619356.7614-16.34517.8672
2758.9343-3.6007-24.71687.22441.523116.9875-0.30180.0709-0.85430.26830.05590.6838-0.2445-0.54070.24590.28920.0643-0.03950.1189-0.08680.201673.7382-23.85629.8537
287.6008-2.14984.06011.039-1.70262.88350.36690.5606-0.4667-0.2203-0.21470.06730.35110.3604-0.15220.2820.0339-0.02740.2028-0.06440.186792.8523-22.282413.3605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 26
3X-RAY DIFFRACTION3A27 - 35
4X-RAY DIFFRACTION4A36 - 41
5X-RAY DIFFRACTION5A42 - 51
6X-RAY DIFFRACTION6A52 - 57
7X-RAY DIFFRACTION7A58 - 71
8X-RAY DIFFRACTION8A72 - 78
9X-RAY DIFFRACTION9A79 - 83
10X-RAY DIFFRACTION10A84 - 89
11X-RAY DIFFRACTION11A90 - 107
12X-RAY DIFFRACTION12A108 - 116
13X-RAY DIFFRACTION13A117 - 122
14X-RAY DIFFRACTION14A123 - 133
15X-RAY DIFFRACTION15B5 - 10
16X-RAY DIFFRACTION16B11 - 24
17X-RAY DIFFRACTION17B25 - 34
18X-RAY DIFFRACTION18B35 - 38
19X-RAY DIFFRACTION19B39 - 49
20X-RAY DIFFRACTION20B50 - 58
21X-RAY DIFFRACTION21B59 - 70
22X-RAY DIFFRACTION22B71 - 78
23X-RAY DIFFRACTION23B79 - 87
24X-RAY DIFFRACTION24B88 - 98
25X-RAY DIFFRACTION25B99 - 110
26X-RAY DIFFRACTION26B111 - 118
27X-RAY DIFFRACTION27B119 - 123
28X-RAY DIFFRACTION28B124 - 133

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