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- PDB-2dak: Solution Structure of the Second UBA Domain in the Human Ubiquiti... -

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Basic information

Entry
Database: PDB / ID: 2dak
TitleSolution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsHYDROLASE / isopeptidase T / Ubiquitin Specific Protease 5 / USP 5 / UBA domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


deubiquitinase activity / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome ...deubiquitinase activity / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin-associated (UBA) domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / UBA-like domain / : / Ubiquitin-associated (UBA) domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsZhao, C. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the Second UBA Domain in the Human Ubiquitin Specific Protease 5 (Isopeptidase 5)
Authors: Zhao, C. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionDec 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: Ubiquitin carboxyl-terminal hydrolase 5


Theoretical massNumber of molelcules
Total (without water)6,5191
Polymers6,5191
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 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 5 / Ubiquitin thiolesterase 5 / Ubiquitin-specific processing protease 5 / Deubiquitinating enzyme 5 / ...Ubiquitin thiolesterase 5 / Ubiquitin-specific processing protease 5 / Deubiquitinating enzyme 5 / Isopeptidase T


Mass: 6519.079 Da / Num. of mol.: 1 / Fragment: UBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: USP5 / Plasmid: P050704-16 / Production host: Cell free synthesis / References: UniProt: P45974, 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: 0.84mM UBA domain U-15N, 13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9321Kobayashi, N.data analysis
CYANA1.0.8Guntert, P.structure solution
CYANA1.0.8Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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