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- PDB-8hqb: NMR Structure of OsCIE1-Ubox -

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Basic information

Entry
Database: PDB / ID: 8hqb
TitleNMR Structure of OsCIE1-Ubox
ComponentsU-box domain-containing protein 12
KeywordsPLANT PROTEIN / ubiquitination / Ubox / ligase
Function / homology
Function and homology information


RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / nucleus / cytoplasm
Similarity search - Function
PUB protein, U-box domain, plant / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical ...PUB protein, U-box domain, plant / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
U-box domain-containing protein 12
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Y. / Yu, C.Z. / Lan, W.X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesYSBR-011 China
CitationJournal: Nature / Year: 2024
Title: Release of a ubiquitin brake activates OsCERK1-triggered immunity in rice.
Authors: Wang, G. / Chen, X. / Yu, C. / Shi, X. / Lan, W. / Gao, C. / Yang, J. / Dai, H. / Zhang, X. / Zhang, H. / Zhao, B. / Xie, Q. / Yu, N. / He, Z. / Zhang, Y. / Wang, E.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _pdbx_database_related.content_type
Revision 1.2May 22, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U-box domain-containing protein 12
B: U-box domain-containing protein 12


Theoretical massNumber of molelcules
Total (without water)17,9052
Polymers17,9052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1420 Å2
ΔGint-13 kcal/mol
Surface area10190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein U-box domain-containing protein 12 / Plant U-box protein 12 / OsPUB12 / RING-type E3 ubiquitin transferase PUB12


Mass: 8952.272 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: PUB12, Os06g0102700, LOC_Os06g01304, OSJNBa0075G19.19-1
Production host: Escherichia coli (E. coli)
References: UniProt: Q5VRH9, RING-type E3 ubiquitin transferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D 1H-13C NOESY aliphatic
151isotropic23D 1H-13C NOESY aromatic
1261isotropic23D CBCA(CO)NH
1131isotropic23D HN(CA)CB
1121isotropic23D HNCA
1111isotropic23D HNCO
1101isotropic13D (H)CCH-TOCSY
181isotropic23D 1H-15N TOCSY
171isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] WT-Ubox, 10 mM TRIS, 100 mM sodium chloride, 1 mM PMSF, 2 mM DTT, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMWT-Ubox[U-100% 13C; U-100% 15N]1
10 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
1 mMPMSFnatural abundance1
2 mMDTTnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD28001
Agilent DD2AgilentDD26002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
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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