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- PDB-1whb: Solution structure of the Rhodanese-like domain in human ubiquiti... -

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Basic information

Entry
Database: PDB / ID: 1whb
TitleSolution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8)
ComponentsKIAA0055
KeywordsHYDROLASE / deubiqutinating enzyme / ubpy / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of lysosomal protein catabolic process / endosome organization / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / mitotic cytokinesis / protein deubiquitination ...negative regulation of lysosomal protein catabolic process / endosome organization / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / mitotic cytokinesis / protein deubiquitination / Regulation of FZD by ubiquitination / cellular response to dexamethasone stimulus / Downregulation of ERBB2:ERBB3 signaling / cellular response to nerve growth factor stimulus / regulation of protein stability / Negative regulation of MET activity / SH3 domain binding / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / midbody / ubiquitinyl hydrolase 1 / Ras protein signal transduction / cysteine-type deubiquitinase activity / early endosome / postsynaptic density / endosome membrane / Ub-specific processing proteases / cadherin binding / cysteine-type endopeptidase activity / glutamatergic synapse / proteolysis / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / : / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / : / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8)
Authors: Saito, K. / 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA0055


Theoretical massNumber of molelcules
Total (without water)17,4911
Polymers17,4911
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA0055 / ubiquitin specific protease 8 / UBP8


Mass: 17490.764 Da / Num. of mol.: 1 / Fragment: Rhodanese-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA ha01049 / Plasmid: P040119-91 / References: UniProt: P40818, 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 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM protein, 20mM d-Tris-HCl, pH 7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / 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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson B.A.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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