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- PDB-8ysy: Ubiquitin(native) from Oryza sativa subsp. japonica (Rice) -

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Basic information

Entry
Database: PDB / ID: 8ysy
TitleUbiquitin(native) from Oryza sativa subsp. japonica (Rice)
ComponentsUbiquitin
KeywordsPLANT PROTEIN / ubiquitin / monomer
Function / homology
Function and homology information


modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40z fusion protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodSOLUTION NMR / simulated annealing / water refinement
AuthorsAdhada, S.T. / Sarma, S.P.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)LSII-022 India
Department of Science & Technology (DST, India)LSII-039/2015 India
Department of Biotechnology (DBT, India)BT/01/CEIB/11/V/17 India
CitationJournal: Biochemistry / Year: 2024
Title: Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model.
Authors: Adhada, S.T. / Sarma, S.P.
History
DepositionMar 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 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: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,6681
Polymers8,6681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin


Mass: 8667.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Ub-CEP52-1, UBQ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CH34
Has protein modificationN

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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
122isotropic23D CBCA(CO)NH
132isotropic23D HN(CA)CB
142isotropic23D C(CO)NH
152isotropic23D 1H-15N TOCSY
162isotropic13D 1H-13C NOESY
172isotropic13D 1H-15N NOESY
182isotropic13D H(CCO)NH
192isotropic11D DOSY
1102isotropic13D HNCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] Ubiquitin from Rice (Oryza sativa), 90% H2O/10% D2OOsubq_N_15N90% H2O/10% D2O
solution21 mM [U-13C; U-15N] Ubiquitin from Rice (Oryza sativa), 90% H2O/10% D2OOsubq_N_13C_15N90% H2O/10% D2O
solution31 mM Ubiquitin from Rice (Oryza sativa), 90% H2O/10% D2OOsubq_N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUbiquitin from Rice (Oryza sativa)[U-15N]1
1 mMUbiquitin from Rice (Oryza sativa)[U-13C; U-15N]2
1 mMUbiquitin from Rice (Oryza sativa)natural abundance3
Sample conditionsIonic strength: 25 mM / Label: native condition / pH: 6.8 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent Direct DriveAgilentDirect Drive6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNchemical shift assignment
CYANA3.98.15Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH3.4Schwieters, Kuszewski, Tjandra and Clorerefinement
VnmrJ4.2Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinalDetails
simulated annealing2structures were calculated using automated NOE assignment protocol with 15N NOEs assigned and 13C NOEs unassigned
water refinement3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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