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- PDB-2lbc: solution structure of tandem UBA of USP13 -

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Basic information

Entry
Database: PDB / ID: 2lbc
Titlesolution structure of tandem UBA of USP13
ComponentsUbiquitin carboxyl-terminal hydrolase 13
KeywordsHYDROLASE / tandem UBA of USP13
Function / homology
Function and homology information


protein K29-linked deubiquitination / protein K6-linked deubiquitination / maintenance of unfolded protein / positive regulation of ERAD pathway / melanocyte differentiation / BAT3 complex binding / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / proteasome binding / ubiquitin-like protein ligase binding ...protein K29-linked deubiquitination / protein K6-linked deubiquitination / maintenance of unfolded protein / positive regulation of ERAD pathway / melanocyte differentiation / BAT3 complex binding / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / proteasome binding / ubiquitin-like protein ligase binding / protein deubiquitination / ubiquitin binding / regulation of protein stability / autophagy / Regulation of PTEN stability and activity / protein-folding chaperone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell population proliferation / regulation of autophagy / protein stabilization / Ub-specific processing proteases / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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. ...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 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsZhang, Y. / Zhou, C. / Zhou, Z. / Song, A. / Hu, H.
CitationJournal: Plos One / Year: 2011
Title: Domain Analysis Reveals That a Deubiquitinating Enzyme USP13 Performs Non-Activating Catalysis for Lys63-Linked Polyubiquitin.
Authors: Zhang, Y. / Zhou, C. / Zhou, Z. / Song, A. / Hu, H.
History
DepositionMar 29, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 13


Theoretical massNumber of molelcules
Total (without water)13,7691
Polymers13,7691
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)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 13 / Deubiquitinating enzyme 13 / Isopeptidase T-3 / ISOT-3 / Ubiquitin thiolesterase 13 / Ubiquitin- ...Deubiquitinating enzyme 13 / Isopeptidase T-3 / ISOT-3 / Ubiquitin thiolesterase 13 / Ubiquitin-specific-processing protease 13


Mass: 13769.251 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 652-777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP13, ISOT3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92995, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HN(CA)CB
1423D C(CO)NH
1513D HNHA
1623D (H)CCH-TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate-1, 50 mM sodium chloride-2, 1 mM [U-100% 15N] entity-3, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate-4, 50 mM sodium chloride-5, 1 mM [U-100% 13C; U-100% 15N] entity-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
1 mMentity-3[U-100% 15N]1
20 mMsodium phosphate-42
50 mMsodium chloride-52
1 mMentity-6[U-100% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIA2.0Linge, O'Donoghue and Nilgesstructure solution
ARIA2.0Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

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