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- PDB-9r2s: Structure of the S.aureus ClpP degradation chamber in the context... -

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Basic information

Entry
Database: PDB / ID: 9r2s
TitleStructure of the S.aureus ClpP degradation chamber in the context of the MecA/ClpC/CLpC complex
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsCHAPERONE / protein-quality control / AAA+ unfoldases / peptidase / adaptor proteins
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsAzinas, S. / Wallden, K. / Katikaridis, P. / Schahl, A. / Mogk, A. / Carroni, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
The Swedish Foundation for Strategic Research Sweden
Citation
Journal: Commun Biol / Year: 2025
Title: Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP.
Authors: Stavros Azinas / Karin Wallden / Panagiotis Katikaridis / Timo Jenne / Adrien Schahl / Axel Mogk / Marta Carroni /
Abstract: Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are ...Bacterial AAA+ proteases are composed of a AAA+ partner (e.g., ClpC) and an associated peptidase (e.g., ClpP). They represent ATP-fuelled and self-compartmentalized proteolytic machines that are crucial for stress resistance and virulence. ClpC requires cooperation with adaptor proteins such as MecA for activation and complex formation with ClpP. Here, we present the cryo-EM structure of the MecA/ClpC/ClpP complex from the major pathogen Staphylococcus aureus. MecA forms a dynamic crown on top of the ClpC/ClpP complex with its substrate-binding domain positioned near the ClpC pore site, likely facilitating substrate transfer. ClpC/ClpP complex formation involves ClpC P-loops and ClpP N-terminal β-hairpins, which insert into the central ClpC threading channel and contact sites next to the ClpC ATPase center. ClpC and ClpP interactions are asymmetric and dictated by the activity states of ClpC ATPase subunits. ClpP binding increases ClpC ATPase and threading activities in a β-hairpin dependent manner, illuminating an allosteric pathway in the cooperation of ATPase and peptidase components in bacterial AAA+ proteases.
#1: Journal: Biorxiv / Year: 2025
Title: Structure of the central Staphylococcus aureus AAA+ protease MecA/ClpC/ClpP
Authors: Azinas, S. / Wallden, K. / Katikaridis, P. / Jenne, T. / Schahl, A. / Mogk, A. / Carroni, M.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Pb: ATP-dependent Clp protease proteolytic subunit
Pe: ATP-dependent Clp protease proteolytic subunit
Pa: ATP-dependent Clp protease proteolytic subunit
Pc: ATP-dependent Clp protease proteolytic subunit
Pd: ATP-dependent Clp protease proteolytic subunit
Pg: ATP-dependent Clp protease proteolytic subunit
Po: ATP-dependent Clp protease proteolytic subunit
Pf: ATP-dependent Clp protease proteolytic subunit
Pq: ATP-dependent Clp protease proteolytic subunit
Pi: ATP-dependent Clp protease proteolytic subunit
Pn: ATP-dependent Clp protease proteolytic subunit
Pm: ATP-dependent Clp protease proteolytic subunit
Ph: ATP-dependent Clp protease proteolytic subunit
Pl: ATP-dependent Clp protease proteolytic subunit


Theoretical massNumber of molelcules
Total (without water)301,51114
Polymers301,51114
Non-polymers00
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 proteolytic subunit / Endopeptidase Clp


Mass: 21536.531 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAB0722 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YSF8, endopeptidase Clp
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: Complex of 14 copies of S.aureus ClpP in the context of the MecA/ClpC/ClpP complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.150 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2200 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2851121
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82834 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003520236
ELECTRON MICROSCOPYf_angle_d0.690927315
ELECTRON MICROSCOPYf_chiral_restr0.04753181
ELECTRON MICROSCOPYf_plane_restr0.00913561
ELECTRON MICROSCOPYf_dihedral_angle_d14.76977636

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