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- PDB-6xqc: UbKEKS -

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Basic information

Entry
Database: PDB / ID: 6xqc
TitleUbKEKS
ComponentsPolyubiquitin-B
KeywordsPROTEIN BINDING / Ubiquitin / alternative protein / post-translational modification
Function / homology
Function and homology information


modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDelattre, P. / Letourneau, D. / Lavigne, P. / Roucou, X. / Boisvert, F.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)398925 Canada
CitationJournal: To Be Published
Title: Solution NMR structure of UbKEKS
Authors: Delattre, P. / Letourneau, D. / Roucou, X. / Boisvert, F.M. / Lavigne, P.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)8,5521
Polymers8,5521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Polyubiquitin-B


Mass: 8551.841 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Expression vector pET-mod (others) / References: UniProt: J3QS39

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D C(CO)NH
172isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
192isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM [U-13C; U-15N] UbKEKS, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution2500 uM [U-13C; U-15N] UbKEKS, 100% D2O15N_13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMUbKEKS[U-13C; U-15N]1
500 uMUbKEKS[U-13C; U-15N]2
Sample conditionsDetails: 50 mM Sodium/potassium phosphate 50 mM NaCl / Ionic strength: 100 mM / Ionic strength err: 5 / Label: standard_conditions / pH: 7.4 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6Bruker Biospinprocessing
ARIA2alphaAriastructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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