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- PDB-6khv: Solution Structure of the CS2 Domain of USP19 -

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Basic information

Entry
Database: PDB / ID: 6khv
TitleSolution Structure of the CS2 Domain of USP19
ComponentsUbiquitin carboxyl-terminal hydrolase 19
KeywordsHYDROLASE / CS domain / HSP90
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. / 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. ...Linker region of USP19 deubiquitinase / CS domain / CS domain / CS domain profile. / 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
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsXue, W. / Hu, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31870764 China
CitationJournal: Biochem.J. / Year: 2020
Title: Domain interactions reveal auto-inhibition of the deubiquitinating enzyme USP19 and its activation by HSP90 in the modulation of huntingtin aggregation.
Authors: Xue, W. / Zhang, S.X. / He, W.T. / Hong, J.Y. / Jiang, L.L. / Hu, H.Y.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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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)13,3381
Polymers13,3381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, SEC
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 13338.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP19, KIAA0891, ZMYND9 / Production host: Escherichia coli (E. coli) / References: UniProt: O94966, ubiquitinyl hydrolase 1

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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 CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D H(CCO)NH
152isotropic13D HNHA
182isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
161isotropic13D (H)CCH-TOCSY
191isotropic13D HNCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] CS2(273-386), 20 mM sodium phosphate, 50 mM sodium chloride, 0.05 mM sodium azide, 90 % v/v H2O, 10 % v/v D2O, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution20.8 mM [U-99% 15N] CS2(273-386), 20 mM sodium phosphate, 50 mM sodium chloride, 0.05 mM sodium azide, 90 % v/v H2O, 10 % v/v D2O, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMCS2(273-386)[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.05 mMsodium azidenatural abundance1
90 % v/vH2Onatural abundance1
10 % v/vD2Onatural abundance1
0.8 mMCS2(273-386)[U-99% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.05 mMsodium azidenatural abundance2
90 % v/vH2Onatural abundance2
10 % v/vD2Onatural abundance2
Sample conditionsIonic strength: 0.08 M / Label: conditions_1 / pH: 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
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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