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- EMDB-53879: Structure of the S.aureus MecA/ClpC/ClpP degradation system -

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Basic information

Entry
Database: EMDB / ID: EMD-53879
TitleStructure of the S.aureus MecA/ClpC/ClpP degradation system
Map dataComposite map of the MecA/ClpC/ClpP complex from S. aureus
Sample
  • Complex: Complex of 6 copies of S.aureus ClpC (without the N terminal and M-domain) plus 14 copies of S.aureus ClpP
    • Protein or peptide: Adapter protein MecA
    • Protein or peptide: unknown substrate
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordsprotein-quality control / AAA+ unfoldases / peptidases / adaptor proteins / CHAPERONE
Function / homology
Function and homology information


stress response to cadmium ion / stress response to copper ion / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / protein-macromolecule adaptor activity / serine-type endopeptidase activity / ATP hydrolysis activity ...stress response to cadmium ion / stress response to copper ion / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / protein-macromolecule adaptor activity / serine-type endopeptidase activity / ATP hydrolysis activity / 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 repeat (R) N-terminal domain / : / ClpP, Ser active site / Endopeptidase Clp serine active site. / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / 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 / 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) / ClpP/crotonase-like domain superfamily / 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 proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit ClpC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAzinas S / Wallden K / Katikaridis P / Schahl A / Mogk A / Carroni M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: 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.
History
DepositionMay 20, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53879.png

Downloads & links

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Map

FileDownload / File: emd_53879.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the MecA/ClpC/ClpP complex from S. aureus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 400 pix.
= 397.6 Å		0.99 Å/pix.
x 400 pix.
= 397.6 Å		0.99 Å/pix.
x 400 pix.
= 397.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.994 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0043234336 - 2.3664694
Average (Standard dev.)0.0020225034 (±0.030717267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 397.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite map of the MecA/ClpC/ClpP complex from S....

Fileemd_53879_additional_1.map
AnnotationComposite map of the MecA/ClpC/ClpP complex from S. aureus sharpened with EMready
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 6 copies of S.aureus ClpC (without the N terminal and ...

EntireName: Complex of 6 copies of S.aureus ClpC (without the N terminal and M-domain) plus 14 copies of S.aureus ClpP
Components
  • Complex: Complex of 6 copies of S.aureus ClpC (without the N terminal and M-domain) plus 14 copies of S.aureus ClpP
    • Protein or peptide: Adapter protein MecA
    • Protein or peptide: unknown substrate
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit ClpC
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of 6 copies of S.aureus ClpC (without the N terminal and ...

SupramoleculeName: Complex of 6 copies of S.aureus ClpC (without the N terminal and M-domain) plus 14 copies of S.aureus ClpP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 800 KDa

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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 aureus (bacteria)
Molecular weightTheoretical: 28.35417 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: unknown substrate

MacromoleculeName: unknown substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 1.549902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #3: ATP-dependent Clp protease ATP-binding subunit ClpC

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit ClpC / type: protein_or_peptide / ID: 3 / Number of copies: 6 / 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 #4: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 4 / 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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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
SoftwareName: EPU (ver. 3.7)
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 correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 82854
Initial angle assignmentType: OTHER / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)

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Atomic model buiding 1

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

PDB-9rai:
Structure of the S.aureus MecA/ClpC/ClpP degradation system

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