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- PDB-2l2d: Solution NMR Structure of human UBA-like domain of OTUD7A_11_83, ... -

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Basic information

Entry
Database: PDB / ID: 2l2d
TitleSolution NMR Structure of human UBA-like domain of OTUD7A_11_83, NESG target HT6304A/OCSP target OTUD7A_11_83/SGC-Toronto
ComponentsOTU domain-containing protein 7A
KeywordsHYDROLASE / uba fold / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP / SGC
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / protein deubiquitination / negative regulation of canonical NF-kappaB signal transduction / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 ...cysteine-type deubiquitinase activity => GO:0004843 / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / protein deubiquitination / negative regulation of canonical NF-kappaB signal transduction / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cezanne-2 peptidase / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / UBA-like domain / OTU domain / OTU domain profile. / Ubiquitin-associated (UBA) domain ...Cezanne-2 peptidase / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / UBA-like domain / OTU domain / OTU domain profile. / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
OTU domain-containing protein 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Lemak, A. / Gutmanas, A. / Houliston, S. / Semesi, A. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) ...Wu, B. / Yee, A. / Lemak, A. / Gutmanas, A. / Houliston, S. / Semesi, A. / Dhe-Paganon, S. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The amino-terminal UBA domain of OTUD7A
Authors: Wu, B. / Asinas, A. / Yee, A. / Doherty, R. / Lemak, A. / Gutmanas, A. / Houliston, S. / Semesi, A. / Arrowsmith, C.H. / Montelione, G.T. / Dhe-Paganon, S.
History
DepositionAug 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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
Revision 1.5May 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: OTU domain-containing protein 7A


Theoretical massNumber of molelcules
Total (without water)8,0461
Polymers8,0461
Non-polymers00
Water0
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 OTU domain-containing protein 7A / Zinc finger protein Cezanne 2


Mass: 8045.925 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUD7A, C15orf16, CEZANNE2, OTUD7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TE49, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] OTUD7A_11_83, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-10% 13C; U-99% 15N] OTUD7A_11_83, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMOTUD7A_11_83-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
10 mMbenzamidine-61
1 %inhibitor cocktail-71
0.5 mMOTUD7A_11_83-8[U-10% 13C; U-99% 15N]2
10 mMTRIS-9[U-100% 2H]2
300 mMsodium chloride-102
10 uMzinc sulphate-112
10 mMDTT-12[U-100% 2H]2
10 mMbenzamidine-132
1 %inhibitor cocktail-142
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
FMCGUI2.4Lemak, Arrowsmithstructure refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
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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