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- EMDB-51498: Structure of the S.aureus MecA protein, in complex with ClpC -

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Basic information

Entry
Database: EMDB / ID: EMD-51498
TitleStructure of the S.aureus MecA protein, in complex with ClpC
Map data
Sample
  • Complex: N-terminal part of the complex between the AAA+ unfoldase ClpC and the adaptor protein MecA from S.aureus.
    • Protein or peptide: Adapter protein MecA
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
Keywordsproteolysis / AAA+ adaptor protein / S.aureus / CHAPERONE
Function / homology
Function and homology information


peptidase activity / cellular response to heat / protein-macromolecule adaptor activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / 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 ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / 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
Adapter protein MecA / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria) / Staphylococcus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCarroni M / Azinas S
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2021.0347 Sweden
The Swedish Foundation for Strategic ResearchRIF21-0047 Sweden
CitationJournal: To Be Published
Title: ClpC and ClpP act as reciprocal allosteric activators to form a highly efficient AAA+ protease
Authors: Azinas S / Wallden K / Katikaridis P / Schahl A / Mogk A / Carroni M
History
DepositionSep 6, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51498.png

Downloads & links

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Map

FileDownload / File: emd_51498.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 304 pix.
= 321.936 Å		1.06 Å/pix.
x 304 pix.
= 321.936 Å		1.06 Å/pix.
x 304 pix.
= 321.936 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: 1.95
Minimum - Maximum-0.58222675 - 16.961266999999999
Average (Standard dev.)0.004484597 (±0.4418023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 321.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51498_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_51498_additional_1.map
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Additional map: #1

Fileemd_51498_additional_2.map
Projections & Slices
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Half map: #2

Fileemd_51498_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51498_half_map_2.map
Projections & Slices
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Sample components

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Entire : N-terminal part of the complex between the AAA+ unfoldase ClpC an...

EntireName: N-terminal part of the complex between the AAA+ unfoldase ClpC and the adaptor protein MecA from S.aureus.
Components
  • Complex: N-terminal part of the complex between the AAA+ unfoldase ClpC and the adaptor protein MecA from S.aureus.
    • Protein or peptide: Adapter protein MecA
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC

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Supramolecule #1: N-terminal part of the complex between the AAA+ unfoldase ClpC an...

SupramoleculeName: N-terminal part of the complex between the AAA+ unfoldase ClpC and the adaptor protein MecA from S.aureus.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: This is referred in the paper as the MecA crown and includes only the N-terminal and coiled-coil part of ClpC.
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Adapter protein MecA

MacromoleculeName: Adapter protein MecA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus (bacteria)
Molecular weightTheoretical: 28.35417 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MRIERVDDTT VKLFITYSDI EARGFSREDL WTNRKRGEEF FWSMMDEINE EEDFVVEGPL WIQVHAFEKG VEVTISKSKN EDMMNMSDD DATDQFDEQV QELLAQTLEG EDQLEELFEQ RTKEKEAQGS KRQKSSARKN TRTIIVKFND LEDVINYAYH S NPITTEFE ...String:
MRIERVDDTT VKLFITYSDI EARGFSREDL WTNRKRGEEF FWSMMDEINE EEDFVVEGPL WIQVHAFEKG VEVTISKSKN EDMMNMSDD DATDQFDEQV QELLAQTLEG EDQLEELFEQ RTKEKEAQGS KRQKSSARKN TRTIIVKFND LEDVINYAYH S NPITTEFE DLLYMVDGTY YYAVYFDSHV DQEVINDSYS QLLEFAYPTD RTEVYLNDYA KIIMSHNVTA QVRRYFPETT E

UniProtKB: Adapter protein MecA

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Macromolecule #2: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 24.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio SGD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82800
Initial angle assignmentType: OTHER / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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