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

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Basic information

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
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, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Additional map: #1

Fileemd_53538_additional_1.map
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Histogram

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Half map: #2

Fileemd_53538_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53538_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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