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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
CitationJournal: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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