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- PDB-6kcz: Solution structure of the ZnF-UBP domain of USP20/VDU2 -

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Basic information

Entry
Database: PDB / ID: 6kcz
TitleSolution structure of the ZnF-UBP domain of USP20/VDU2
ComponentsUbiquitin carboxyl-terminal hydrolase 20
KeywordsHYDROLASE
Function / homology
Function and homology information


protein K48-linked deubiquitination / regulation of G protein-coupled receptor signaling pathway / protein K63-linked deubiquitination / protein deubiquitination / G protein-coupled receptor binding / endocytosis / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases ...protein K48-linked deubiquitination / regulation of G protein-coupled receptor signaling pathway / protein K63-linked deubiquitination / protein deubiquitination / G protein-coupled receptor binding / endocytosis / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / centrosome / perinuclear region of cytoplasm / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Ubiquitin specific protease (USP) domain signature 2. ...Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y. / Wen, Y. / Zhang, N.
CitationJournal: Protein Sci. / Year: 2019
Title: Structural and functional studies of USP20 ZnF-UBP domain by NMR.
Authors: Yang, Y. / Ding, Y. / Zhou, C. / Wen, Y. / Zhang, N.
History
DepositionJun 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
SupersessionAug 21, 2019ID: 5Z4I
Revision 1.1Aug 21, 2019Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
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 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0814
Polymers10,8841
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6230 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 20 / Deubiquitinating enzyme 20 / Ubiquitin thioesterase 20 / Ubiquitin-specific-processing protease 20 ...Deubiquitinating enzyme 20 / Ubiquitin thioesterase 20 / Ubiquitin-specific-processing protease 20 / VHL-interacting deubiquitinating enzyme 2 / hVDU2


Mass: 10884.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP20, KIAA1003, LSFR3A, VDU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2K6, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
182isotropic13D 1H-15N NOESY
193isotropic12D 1H-13C HSQC
1103isotropic13D 1H-13C NOESY aliphatic
1113isotropic13D (H)CCH-TOCSY
1121isotropic13D H(CCO)NH
1131isotropic13D C(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-99% 13C; U-99% 15N] USP20, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution20.6 mM [U-99% 15N] USP20, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution30.6 mM [U-99% 13C] USP20, 100% D2O13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMUSP20[U-99% 13C; U-99% 15N]1
0.6 mMUSP20[U-99% 15N]2
0.6 mMUSP20[U-99% 13C]3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 Pa / 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
CNSBrunger A. T. et.al.refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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