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- EMDB-53312: S.aureus ClpC decameric resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-53312
TitleS.aureus ClpC decameric resting state
Map dataCryoEM raw map of ClpC S. aureus resting state 10mer.
Sample
  • Complex: ClpC decameric resting state
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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
ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsEngelhardt L / Carroni M
Funding support Sweden, 1 items
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, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53312.png

Downloads & links

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Map

FileDownload / File: emd_53312.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM raw map of ClpC S. aureus resting state 10mer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 324 pix.
= 536.544 Å		1.66 Å/pix.
x 324 pix.
= 536.544 Å		1.66 Å/pix.
x 324 pix.
= 536.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0593
Minimum - Maximum-0.08474283 - 0.43029857
Average (Standard dev.)0.00024275744 (±0.013124477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 536.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM sharpened map by cryoSPARC of ClpC S....

Fileemd_53312_additional_1.map
AnnotationCryoEM sharpened map by cryoSPARC of ClpC S. aureus resting state 10mer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM sharpened map by emReady of ClpC S....

Fileemd_53312_additional_2.map
AnnotationCryoEM sharpened map by emReady of ClpC S. aureus resting state 10mer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of ClpC S. aureus resting state 10mer.

Fileemd_53312_half_map_1.map
AnnotationHalf map A of ClpC S. aureus resting state 10mer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of ClpC S. aureus resting state 10mer.

Fileemd_53312_half_map_2.map
AnnotationHalf map B of ClpC S. aureus resting state 10mer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ClpC decameric resting state

EntireName: ClpC decameric resting state
Components
  • Complex: ClpC decameric resting state
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ClpC decameric resting state

SupramoleculeName: ClpC decameric resting state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 910 KDa

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

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 91.170352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLFGRLTERA QRVLAHAQEE AIRLNHSNIG TEHLLLGLMK EPEGIAAKVL ESFNITEDKV IEEVEKLIGH GQDHVGTLHY TPRAKKVIE LSMDEARKLH HNFVGTEHIL LGLIRENEGV AARVFANLDL NITKARAQVV KALGNPEMSN KNAQASKSNN T PTLDSLAR ...String:
MLFGRLTERA QRVLAHAQEE AIRLNHSNIG TEHLLLGLMK EPEGIAAKVL ESFNITEDKV IEEVEKLIGH GQDHVGTLHY TPRAKKVIE LSMDEARKLH HNFVGTEHIL LGLIRENEGV AARVFANLDL NITKARAQVV KALGNPEMSN KNAQASKSNN T PTLDSLAR DLTVIAKDGT LDPVIGRDKE ITRVIEVLSR RTKNNPVLIG EPGVGKTAIA EGLAQAIVNN EVPETLKDKR VM SLDMGTV VAGTKYRGEF EERLKKVMEE IQQAGNVILF IDELHTLVGA GGAEGAIDAS NILKPALARG ELQCIGATTL DEY RKNIEK DAALERRFQP VQVDEPSVVD TVAILKGLRD RYEAHHRINI SDEAIEAAVK LSNRYVSDRF LPDKAIDLID EASS KVRLK SHTTPNNLKE IEQEIEKVKN EKDAAVHAQE FENAANLRDK QTKLEKQYEE AKNEWKNAQN GMSTSLSEED IAEVI AGWT GIPLTKINET ESEKLLSLED TLHERVIGQK DAVNSISKAV RRARAGLKDP KRPIGSFIFL GPTGVGKTEL ARALAE SMF GDDDAMIRVD MSEFMEKHAV SRLVGAPPGY VGHDDGGQLT EKVRRKPYSV ILFDEIEKAH PDVFNILLQV LDDGHLT DT KGRTVDFRNT IIIMTSNVGA QELQDQRFAG FGGSSDGQDY ETIRKTMLKE LKNSFRPEFL NRVDDIIVFH KLTKEELK E IVTMMVNKLT NRLSEQNINI IVTDKAKDKI AEEGYDPEYG ARPLIRAIQK TIEDNLSELI LDGNQIEGKK VTVDHDGKE FKYDIAEQTS ETKTPSQA

UniProtKB: ATP-dependent Clp protease ATP-binding subunit ClpC

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMTrisTrisaminomethane
25.0 mMKClPotassium Chloride
10.0 mMMgCl2Magnesium Chloride
1.0 mMDTTDithiothreitol
2.0 mMATPAdenosine Triphosphate

Details: 25mM Tris, 25mM KCl, 10mM MgCl2, 1mM DTT, 2mM ATP
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 40000000.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297.15 K / Instrument: FEI VITROBOT MARK IV
Details: ClpC WT was incubated at 10uM for 10 minutes at room temperature prior to vitrification..

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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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1301397
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: SGD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181306
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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