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- PDB-8p66: Structural basis of aggregate binding/recognition by the AAA+ dis... -

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Basic information

Entry
Database: PDB / ID: 8p66
TitleStructural basis of aggregate binding/recognition by the AAA+ disaggregase ClpG
ComponentsClp protease ClpC,Heat shock survival AAA family ATPase ClpK
KeywordsCHAPERONE / ATPase associated with diverse cellular activities (AAA) / protein aggregation / molecular chaperone / stress / 70 kilodalton heat shock protein (Hsp70)
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal ...ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heat shock survival AAA family ATPase ClpK
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSimon, B. / Hennig, J. / Mogk, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)MO970/7-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural basis of aggregate binding by the AAA+ disaggregase ClpG.
Authors: Katikaridis, P. / Simon, B. / Jenne, T. / Moon, S. / Lee, C. / Hennig, J. / Mogk, A.
History
DepositionMay 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Clp protease ClpC,Heat shock survival AAA family ATPase ClpK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4582
Polymers6,3921
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Clp protease ClpC,Heat shock survival AAA family ATPase ClpK


Mass: 6392.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: BI380_06745, clpK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B1YGD3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCA
161isotropic13D (H)CCH-TOCSY
171isotropic13D HNCO
181isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] ClpG, 95% H2O/5% D2O
Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: ClpG / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: KCl 50mM mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2Linge, O'Donoghue and Nilgesstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3 / Details: refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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