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- PDB-9qqr: S.aureus ClpC decameric resting state -

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Basic information

Entry
Database: PDB / ID: 9qqr
TitleS.aureus ClpC decameric resting state
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC
KeywordsCHAPERONE / AAA+ / Unfoldase
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / ATP hydrolysis activity / ATP binding
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : ...UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsEngelhardt, L. / Carroni, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: EMBO J / Year: 2025
Title: Allosteric control of the bacterial ClpC/ClpP protease and its hijacking by antibacterial peptides.
Authors: Timo Jenne / Lisa Engelhardt / Ieva Baronaite / Dorit Levy / Inbal Riven / Maciej Malolepszy / Stavros Azinas / Taras Sych / Erdinc Sezgin / Dirk Flemming / Irmgard Sinning / Gilad Haran / ...Authors: Timo Jenne / Lisa Engelhardt / Ieva Baronaite / Dorit Levy / Inbal Riven / Maciej Malolepszy / Stavros Azinas / Taras Sych / Erdinc Sezgin / Dirk Flemming / Irmgard Sinning / Gilad Haran / Marta Carroni / Axel Mogk /
Abstract: The hexameric AAA+ protein ClpC, combined with peptidase ClpP, forms a critical ATP-dependent protease in bacteria, essential for virulence. ClpC is usually repressed in an inactive resting state, ...The hexameric AAA+ protein ClpC, combined with peptidase ClpP, forms a critical ATP-dependent protease in bacteria, essential for virulence. ClpC is usually repressed in an inactive resting state, where two ClpC spirals interact via coiled-coil M-domains. Antibacterial peptides and partner proteins trigger ClpC activation by binding to its N-terminal domain (NTD). This study reveals that the NTD stabilizes the resting state through multiple anchoring points to M-domains and ATPase domains. The same NTD sites also serve as binding sites for adaptor proteins and substrates carrying phosphorylated arginines (pArg), disrupting resting state interactions and promoting active ClpC hexamer formation. This coupling ensures that ClpC activation aligns with substrate and partner protein availability. Toxic peptides exploit this regulatory mechanism, leading to continuous ClpC activation and harmful, uncontrolled proteolysis. These findings highlight the dual role of the NTD in maintaining resting state stability and mediating activation, emphasizing its critical role in bacterial protease regulation and its potential as a drug target.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
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Revision 1.1Aug 20, 2025Group: Data collection / Database references / Structure summary
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Revision 1.1Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / pdbx_database_related / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: ATP-dependent Clp protease ATP-binding subunit ClpC
G: ATP-dependent Clp protease ATP-binding subunit ClpC
H: ATP-dependent Clp protease ATP-binding subunit ClpC
I: ATP-dependent Clp protease ATP-binding subunit ClpC
J: ATP-dependent Clp protease ATP-binding subunit ClpC
E: ATP-dependent Clp protease ATP-binding subunit ClpC
D: ATP-dependent Clp protease ATP-binding subunit ClpC
C: ATP-dependent Clp protease ATP-binding subunit ClpC
B: ATP-dependent Clp protease ATP-binding subunit ClpC
A: ATP-dependent Clp protease ATP-binding subunit ClpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)918,83125
Polymers911,70410
Non-polymers7,12815
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpC


Mass: 91170.352 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpC, SAOUHSC_00505 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G0P5
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ClpC decameric resting state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.91 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 25mM Tris, 25mM KCl, 10mM MgCl2, 1mM DTT, 2mM ATP
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisaminomethaneTris1
225 mMPotassium ChlorideKCl1
310 mMMagnesium ChlorideMgCl21
41 mMDithiothreitolDTT1
52 mMAdenosine TriphosphateATP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297.15 K
Details: ClpC WT was incubated at 10uM for 10 minutes at room temperature prior to vitrification.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1301397
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181306 / Symmetry type: POINT
RefinementHighest resolution: 4.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00153862
ELECTRON MICROSCOPYf_angle_d0.34772677
ELECTRON MICROSCOPYf_dihedral_angle_d7.69520966
ELECTRON MICROSCOPYf_chiral_restr0.0388395
ELECTRON MICROSCOPYf_plane_restr0.0029448

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