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- PDB-6gh9: USP15 catalytic domain in complex with small molecule -

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Basic information

Entry
Database: PDB / ID: 6gh9
TitleUSP15 catalytic domain in complex with small molecule
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE / protease / ubiquitin / ubiquitin specific protease / inhibitor / mitoxantrone
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
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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-MIX / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWard, S.J. / Gratton, H.E. / Caulton, S.G. / Emsley, J. / Dreveny, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H012656/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel.
Authors: Ward, S.J. / Gratton, H.E. / Indrayudha, P. / Michavila, C. / Mukhopadhyay, R. / Maurer, S.K. / Caulton, S.G. / Emsley, J. / Dreveny, I.
History
DepositionMay 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)84,0825
Polymers83,4942
Non-polymers5883
Water2,756153
1
A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3354
Polymers41,7471
Non-polymers5883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 15


Theoretical massNumber of molelcules
Total (without water)41,7471
Polymers41,7471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.070, 94.390, 63.290
Angle α, β, γ (deg.)90.000, 90.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 254 through 311 or resid 313...
21(chain B and (resid 254 through 311 or resid 313 through 753 or resid 756 through 911))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 254 through 311 or resid 313...AA254 - 3111 - 58
12TYRTYRLYSLYS(chain A and (resid 254 through 311 or resid 313...AA313 - 77160 - 206
13ALAALAGLYGLY(chain A and (resid 254 through 311 or resid 313...AA789 - 856224 - 291
14HISHISGLYGLY(chain A and (resid 254 through 311 or resid 313...AA862 - 911297 - 346
21METMETLYSLYS(chain B and (resid 254 through 311 or resid 313 through 753 or resid 756 through 911))BB254 - 3111 - 58
22TYRTYRSERSER(chain B and (resid 254 through 311 or resid 313 through 753 or resid 756 through 911))BB313 - 75360 - 188
23LYSLYSGLYGLY(chain B and (resid 254 through 311 or resid 313 through 753 or resid 756 through 911))BB756 - 911191 - 346

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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: 41747.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: catalytic core region (USP15-D1D2) with the insert harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),catalytic core region (USP15-D1D2) ...Details: catalytic core region (USP15-D1D2) with the insert harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),catalytic core region (USP15-D1D2) with the insert harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),catalytic core region (USP15-D1D2) with the insert harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),catalytic core region (USP15-D1D2) with the insert harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO)
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MIX / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE / MITOXANTRONE / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRA-9,10-QUINONE


Mass: 444.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes pH 7.0, 14% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.09→62.07 Å / Num. obs: 42810 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 39.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.052 / Rrim(I) all: 0.115 / Net I/σ(I): 9.9 / Num. measured all: 203657
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.144.91.61931530.6680.8071.81598.6
9.35-62.074.50.0275010.9990.0150.03198.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.29data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y6E

2y6e


Resolution: 2.09→62.07 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.24
RfactorNum. reflection% reflection
Rfree0.2517 2035 4.76 %
Rwork0.2028 --
obs0.2052 42747 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.4 Å2 / Biso mean: 59.0276 Å2 / Biso min: 24.7 Å2
Refinement stepCycle: final / Resolution: 2.09→62.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5123 0 37 153 5313
Biso mean--89.03 50.47 -
Num. residues----640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2896X-RAY DIFFRACTION11.227TORSIONAL
12B2896X-RAY DIFFRACTION11.227TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.13870.37241360.33832696283298
2.1387-2.19210.45451020.3242701280398
2.1921-2.25140.35151250.30172688281398
2.2514-2.31770.33631610.27572681284299
2.3177-2.39250.30321400.25562726286699
2.3925-2.4780.27531440.24592674281899
2.478-2.57720.29291400.24092694283499
2.5772-2.69450.27321210.22232744286599
2.6945-2.83660.2751490.2362673282299
2.8366-3.01430.27911240.2132738286299
3.0143-3.2470.29871290.2052736286599
3.247-3.57370.2551520.18332709286199
3.5737-4.09080.19731190.16672753287299
4.0908-5.15360.18111530.15212737289099
5.1536-62.09730.24531400.19672762290299
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)
16.5142-1.5042-1.26972.3137-0.03143.34790.017-0.2206-0.08820.25120.05770.16660.0307-0.1107-0.04450.2668-0.0727-0.02030.54440.02410.2679-87.712715.337738.751
23.2681-0.6357-0.40543.0943-0.5522.50030.09340.32650.41620.06330.011-0.2109-0.32370.1629-0.1060.28390.00030.02160.57820.0150.2973-78.984428.37727.303
32.73053.08290.26083.4660.20366.76630.0556-0.4197-0.43090.5924-0.3555-0.563-0.0970.62470.22770.27660.0358-0.0350.65230.01680.3798-38.43489.09746.2723
47.0927-1.044-0.30652.7260.8593.81840.098-0.8170.41820.4313-0.0286-0.1289-0.02020.3276-0.03670.2961-0.0935-0.00850.486-0.040.2772-46.723818.7728.6431
53.1638-1.8044-0.20091.33880.59245.67690.045-0.82110.36420.3004-0.45230.80140.4816-1.81590.36970.44730.04520.09280.8782-0.04510.5133-72.014920.47792.4198
66.1526-1.63530.2792.2870.57512.52630.08960.4202-0.76670.0455-0.030.25880.2088-0.1285-0.08050.2499-0.00480.01710.42530.00890.3132-55.9224.6517-5.2422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 254 through 385 )A254 - 385
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 913 )A386 - 913
3X-RAY DIFFRACTION3chain 'B' and (resid 254 through 279 )B254 - 279
4X-RAY DIFFRACTION4chain 'B' and (resid 280 through 366 )B280 - 366
5X-RAY DIFFRACTION5chain 'B' and (resid 367 through 385 )B367 - 385
6X-RAY DIFFRACTION6chain 'B' and (resid 386 through 911 )B386 - 911

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