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- PDB-6ml1: Structure of the USP15 deubiquitinase domain in complex with an a... -

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Basic information

Entry
Database: PDB / ID: 6ml1
TitleStructure of the USP15 deubiquitinase domain in complex with an affinity-matured inhibitory Ubv
Components
  • Proteolyzed N-terminal tag of Ubv.15.1a construct
  • Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
  • Ubiquitin variant 15.1a
KeywordsSIGNALING PROTEIN / deubiuqitination / Ubv / high-affinity / inhibition
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 / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / 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 / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / 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 / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-A / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSinger, A.U. / Teyra, J. / Boehmelt, G. / Lenter, M. / Sicheri, F. / Sidhu, S.S.
CitationJournal: Structure / Year: 2019
Title: Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.
Authors: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / ...Authors: Teyra, J. / Singer, A.U. / Schmitges, F.W. / Jaynes, P. / Kit Leng Lui, S. / Polyak, M.J. / Fodil, N. / Krieger, J.R. / Tong, J. / Schwerdtfeger, C. / Brasher, B.B. / Ceccarelli, D.F.J. / Moffat, J. / Sicheri, F. / Moran, M.F. / Gros, P. / Eichhorn, P.J.A. / Lenter, M. / Boehmelt, G. / Sidhu, S.S.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Feb 8, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr ...database_2 / pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 4, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin variant 15.1a
C: Ubiquitin variant 15.1a
G: Proteolyzed N-terminal tag of Ubv.15.1a construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,80318
Polymers103,1275
Non-polymers67613
Water7,008389
1
A: Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
C: Ubiquitin variant 15.1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4639
Polymers50,0362
Non-polymers4277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin variant 15.1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2858
Polymers50,0362
Non-polymers2496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.770, 115.290, 95.320
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABEC

#1: Protein Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,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: 39753.023 Da / Num. of mol.: 2 / Fragment: 275-470,781-934,275-470,781-934,275-470,781-934
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Plasmid: pHH1013
Details (production host): N-terminal 6-His and Glutathione S-transferase (GST) tag followed by TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin variant 15.1a


Mass: 10282.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a Ubv (ubiquitin variant) selected by phage display to bindthe USP15 USP domain with high affinity
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pET53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0L7RG06

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Protein/peptide , 1 types, 1 molecules G

#3: Protein/peptide Proteolyzed N-terminal tag of Ubv.15.1a construct


Mass: 3055.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Typically this region is removed upon TEV cleavage. TEV cleavage was performed in this case, but I seem to have density which can only be attributed to residues from this proteolyzed N-terminal tag
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET53
Details (production host): N-terminal region of the Ubv ending in a TEV cleavage site
Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 402 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG3350, 100 mM MES 6.0, 250 mM CaCl2, cryoprotected with 18% PEG3350, 200 mM CaCl2, 100 mM MES pH 6.5 and 25% glycerol
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→95.27 Å / Num. obs: 71233 / % possible obs: 98.1 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.031 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3864 / CC1/2: 0.987 / % possible all: 81.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: USP15 and Ubv from 6CRN

6crn


Resolution: 1.9→49.319 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.13
RfactorNum. reflection% reflection
Rfree0.2195 3425 4.81 %
Rwork0.1894 --
obs0.1909 71189 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 27 389 6825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076640
X-RAY DIFFRACTIONf_angle_d0.8178996
X-RAY DIFFRACTIONf_dihedral_angle_d5.5555330
X-RAY DIFFRACTIONf_chiral_restr0.054986
X-RAY DIFFRACTIONf_plane_restr0.0061154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92710.31031240.26322294X-RAY DIFFRACTION80
1.9271-1.95590.29641180.24922522X-RAY DIFFRACTION87
1.9559-1.98650.29771370.23362771X-RAY DIFFRACTION97
1.9865-2.0190.29241380.22562853X-RAY DIFFRACTION100
2.019-2.05390.26341690.20832865X-RAY DIFFRACTION100
2.0539-2.09120.26171200.21382837X-RAY DIFFRACTION100
2.0912-2.13140.26881390.21262944X-RAY DIFFRACTION100
2.1314-2.17490.23861470.21232842X-RAY DIFFRACTION100
2.1749-2.22220.26631590.21192805X-RAY DIFFRACTION100
2.2222-2.27390.29131410.21082909X-RAY DIFFRACTION100
2.2739-2.33080.23511200.20522849X-RAY DIFFRACTION100
2.3308-2.39380.24051320.19842920X-RAY DIFFRACTION99
2.3938-2.46420.22321360.19532846X-RAY DIFFRACTION99
2.4642-2.54380.25221440.20472780X-RAY DIFFRACTION97
2.5438-2.63470.2141710.19842851X-RAY DIFFRACTION100
2.6347-2.74020.25031460.19712864X-RAY DIFFRACTION100
2.7402-2.86490.24431650.19492888X-RAY DIFFRACTION100
2.8649-3.01590.21391400.18632852X-RAY DIFFRACTION100
3.0159-3.20480.25031110.19262904X-RAY DIFFRACTION100
3.2048-3.45220.21071310.18172859X-RAY DIFFRACTION99
3.4522-3.79950.17661710.17642829X-RAY DIFFRACTION98
3.7995-4.3490.19211570.16152894X-RAY DIFFRACTION100
4.349-5.47820.17661610.15822871X-RAY DIFFRACTION100
5.4782-49.33560.20721480.19672915X-RAY DIFFRACTION99

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