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- PDB-6cpm: Structure of the USP15 deubiquitinase domain in complex with a th... -

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Basic information

Entry
Database: PDB / ID: 6cpm
TitleStructure of the USP15 deubiquitinase domain in complex with a third-generation inhibitory Ubv
Components
  • Ubiquitin carboxyl-terminal hydrolase 15
  • Ubiquitin variant 15.1d
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 / 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 / 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-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.011 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
DepositionMar 13, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin carboxyl-terminal hydrolase 15
D: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin variant 15.1d
F: Ubiquitin variant 15.1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,52418
Polymers98,7864
Non-polymers73914
Water9,566531
1
C: Ubiquitin carboxyl-terminal hydrolase 15
F: Ubiquitin variant 15.1d
hetero molecules


  • defined by author&software
  • Evidence: The individual USP15/Ubv complexes aka molecules C+F and D+E are held as a tetrameric complex by residues D860 and Q933 from molecules C and D forming a probably artificial octahedral Ca-binding site.
  • 49.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)49,77910
Polymers49,3932
Non-polymers3868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-36 kcal/mol
Surface area18840 Å2
MethodPISA
2
D: Ubiquitin carboxyl-terminal hydrolase 15
E: Ubiquitin variant 15.1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7468
Polymers49,3932
Non-polymers3536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.552, 115.080, 95.701
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules CDEF

#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: 39753.023 Da / Num. of mol.: 2
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: Protein Ubiquitin variant 15.1d / Ubv 15.1d


Mass: 9639.934 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 bind the USP15 USP domain with high affinity
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 6 types, 545 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16% PEG3350, 100 mM MES, 200 mM CaCl2, cryoprotected with the identical buffer plus 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 22, 2017 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 60994 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.4
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 6036 / CC1/2: 0.767 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: usp15 and Ubv model for the USP15/AM5 structure

Resolution: 2.011→38.205 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2001 3.28 %
Rwork0.1667 --
obs0.1681 60950 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.011→38.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 32 531 7167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076871
X-RAY DIFFRACTIONf_angle_d0.8749307
X-RAY DIFFRACTIONf_dihedral_angle_d4.5345430
X-RAY DIFFRACTIONf_chiral_restr0.0631000
X-RAY DIFFRACTIONf_plane_restr0.0061212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0105-2.06080.27681450.21664079X-RAY DIFFRACTION98
2.0608-2.11650.27991500.20384231X-RAY DIFFRACTION100
2.1165-2.17880.24071320.19134179X-RAY DIFFRACTION100
2.1788-2.24910.25341430.18054195X-RAY DIFFRACTION100
2.2491-2.32950.22561470.17544206X-RAY DIFFRACTION100
2.3295-2.42270.23791420.17664208X-RAY DIFFRACTION100
2.4227-2.5330.22171440.17524208X-RAY DIFFRACTION100
2.533-2.66650.22791430.1764257X-RAY DIFFRACTION100
2.6665-2.83350.22631350.17054200X-RAY DIFFRACTION100
2.8335-3.05220.2331490.17054227X-RAY DIFFRACTION100
3.0522-3.35920.2041420.16464198X-RAY DIFFRACTION100
3.3592-3.84490.20061470.154252X-RAY DIFFRACTION100
3.8449-4.84260.16381410.13874233X-RAY DIFFRACTION100
4.8426-38.21190.19561410.17394276X-RAY DIFFRACTION100

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