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- EMDB-53538: Structure of the S.aureus ClpP degradation chamber in the context... -

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Entry
Database: EMDB / ID: EMD-53538
TitleStructure of the S.aureus ClpP degradation chamber in the context of the MecA/ClpC/CLpC complex
Map data
Sample
  • Complex: Complex of 14 copies of S.aureus ClpP in the context of the MecA/ClpC/ClpP complex
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
Keywordsprotein-quality control / AAA+ unfoldases / peptidase / adaptor proteins / CHAPERONE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsAzinas S / Wallden K / Katikaridis P / Schahl A / Mogk A / Carroni M
Funding support Sweden, 2 items
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, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53538.png

Downloads & links

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Map

FileDownload / File: emd_53538.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 423.6 Å		1.06 Å/pix.
x 400 pix.
= 423.6 Å		1.06 Å/pix.
x 400 pix.
= 423.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.19
Minimum - Maximum-0.95978636 - 21.527305999999999
Average (Standard dev.)-0.0047204806 (±0.41277495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53538_msk_1.map
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Additional map: #1

Fileemd_53538_additional_1.map
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Half map: #2

Fileemd_53538_half_map_1.map
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Half map: #1

Fileemd_53538_half_map_2.map
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Sample components

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Entire : Complex of 14 copies of S.aureus ClpP in the context of the MecA/...

EntireName: Complex of 14 copies of S.aureus ClpP in the context of the MecA/ClpC/ClpP complex
Components
  • Complex: Complex of 14 copies of S.aureus ClpP in the context of the MecA/ClpC/ClpP complex
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit

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Supramolecule #1: Complex of 14 copies of S.aureus ClpP in the context of the MecA/...

SupramoleculeName: Complex of 14 copies of S.aureus ClpP in the context of the MecA/ClpC/ClpP complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 21.536531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLIPTVIET TNRGERAYDI YSRLLKDRII MLGSQIDDNV ANSIVSQLLF LQAQDSEKDI YLYINSPGGS VTAGFAIYDT IQHIKPDVQ TICIGMAASM GSFLLAAGAK GKRFALPNAE VMIHQPLGGA QGQATEIEIA ANHILKTREK LNRILSERTG Q SIEKIQKD ...String:
MNLIPTVIET TNRGERAYDI YSRLLKDRII MLGSQIDDNV ANSIVSQLLF LQAQDSEKDI YLYINSPGGS VTAGFAIYDT IQHIKPDVQ TICIGMAASM GSFLLAAGAK GKRFALPNAE VMIHQPLGGA QGQATEIEIA ANHILKTREK LNRILSERTG Q SIEKIQKD TDRDNFLTAE EAKEYGLIDE VMVPETK

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.6 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2851121
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82834
Initial angle assignmentType: OTHER / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9r2s:
Structure of the S.aureus ClpP degradation chamber in the context of the MecA/ClpC/CLpC complex

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