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- EMDB-53324: S.aureus ClpC dodecameric resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-53324
TitleS.aureus ClpC dodecameric resting state
Map dataCryoEM of ClpC dodecameric resting state of Staphylococcus aureus.
Sample
  • Complex: ClpC 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 amino terminal domain, pathogenicity island component / Clp, repeat (R) 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 amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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: 4.4 Å
AuthorsEngelhardt L / Carroni M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Allosteric control of the bacterial ClpC/ClpP protease and its hijacking by antibacterial peptides
Authors: Jenne T / Engelhardt L / Baronaite I / Levy L / Riven I / Malolepszy M / Azinas S / Sych T / Flemming D / Sinning I / Haran G / Carroni M / Mogk A
History
DepositionApr 4, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53324.png

Downloads & links

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Map

FileDownload / File: emd_53324.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM of ClpC dodecameric resting state of Staphylococcus aureus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 512 pix.
= 496.64 Å		0.97 Å/pix.
x 512 pix.
= 496.64 Å		0.97 Å/pix.
x 512 pix.
= 496.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0764
Minimum - Maximum-0.21596362 - 0.49237594
Average (Standard dev.)0.00015641814 (±0.012953434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 496.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened cryoEM by CryoSparc of ClpC dodecameric resting...

Fileemd_53324_additional_1.map
AnnotationSharpened cryoEM by CryoSparc of ClpC dodecameric resting state of Staphylococcus aureus.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryoEM by emReady of ClpC dodecameric resting...

Fileemd_53324_additional_2.map
AnnotationSharpened cryoEM by emReady of ClpC dodecameric resting state of Staphylococcus aureus.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map B of ClpC dodecameric resting...

Fileemd_53324_half_map_1.map
AnnotationCryoEM half map B of ClpC dodecameric resting state of Staphylococcus aureus.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map A of ClpC dodecameric resting...

Fileemd_53324_half_map_2.map
AnnotationCryoEM half map A of ClpC dodecameric resting state of Staphylococcus aureus.
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 resting state

EntireName: ClpC resting state
Components
  • Complex: ClpC 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 resting state

SupramoleculeName: ClpC 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: 12 / 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: 8 / 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: 9 / 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

Concentration0.6 mg/mL
BufferpH: 7.5 / 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: 500
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179568
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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