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- PDB-1wh0: Solution structure of the CS domain of human USP19 -

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Basic information

Entry
Database: PDB / ID: 1wh0
TitleSolution structure of the CS domain of human USP19
ComponentsUbiquitin carboxyl-terminal hydrolase 19
KeywordsHYDROLASE / USP / CS domain / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / regulation of cellular response to hypoxia / protein deubiquitination / : / response to endoplasmic reticulum stress / Hsp90 protein binding / regulation of protein stability / ubiquitinyl hydrolase 1 ...regulation of ERAD pathway / positive regulation of cell cycle process / negative regulation of skeletal muscle tissue development / regulation of cellular response to hypoxia / protein deubiquitination / : / response to endoplasmic reticulum stress / Hsp90 protein binding / regulation of protein stability / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / endoplasmic reticulum membrane / metal ion binding / cytosol
Similarity search - Function
Linker region of USP19 deubiquitinase / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / HSP20-like chaperone ...Linker region of USP19 deubiquitinase / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / HSP20-like chaperone / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsNakanishi, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the CS domain of human USP19
Authors: Nakanishi, T. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Remark 650HELIX AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 19


Theoretical massNumber of molelcules
Total (without water)14,9141
Polymers14,9141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 19 / Ubiquitin specific protease 19 / Ubiquitin thiolesterase 19 / Ubiquitin-specific processing ...Ubiquitin specific protease 19 / Ubiquitin thiolesterase 19 / Ubiquitin-specific processing protease 19 / Deubiquitinating enzyme 19 / Zinc finger MYND domain containing protein 9


Mass: 14913.787 Da / Num. of mol.: 1 / Fragment: CS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA hk08201 / Plasmid: P040114-29 / References: UniProt: O94966, EC: 3.1.2.15

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.15mM CS domain U-15N, 13C; 20mM NaPi; 100mM NaCl; 2mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.8999Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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