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- EMDB-57170: Cryo-EM structure of the ClpE/ClpP degradation complex from E.faecalis -

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Basic information

Entry
Database: EMDB / ID: EMD-57170
TitleCryo-EM structure of the ClpE/ClpP degradation complex from E.faecalis
Map data
Sample
  • Complex: E. faecalis AAA+ protease ClpE/ClpP complex
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: unknown substrate bound to ClpE/ClpP
    • Protein or peptide: ATP-dependent Clp protease, ATP-binding subunit ClpE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAAA+ chaperone / protease / 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 / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis ...endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidase activity / cellular response to heat / ATPase binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
UVR domain superfamily / 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 / : ...UVR domain superfamily / 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 / : / 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 / 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
ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease, ATP-binding subunit ClpE
Similarity search - Component
Biological speciesEnterobacter (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCarroni M / Mogk A
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
The Swedish Foundation for Strategic Research Sweden
CitationJournal: J Biol Chem / Year: 2026
Title: Structure-function analysis of the bacterial ClpE-ClpP AAA+ protease.
Authors: Mariasole De Rosa / Lisa Maag / Dirk Flemming / Irmgard Sinning / Marta Carroni / Axel Mogk /
Abstract: General and regulatory proteolysis in bacteria is executed by a set of ATP-dependent proteases composed of hexameric ring-forming AAA+ proteins and associated peptidase barrels (e.g., ClpP). These ...General and regulatory proteolysis in bacteria is executed by a set of ATP-dependent proteases composed of hexameric ring-forming AAA+ proteins and associated peptidase barrels (e.g., ClpP). These AAA+ proteases play crucial roles in stress protection and bacterial virulence. Here, we provide the first biochemical characterization of the potential drug target ClpE-ClpP from Enterococcus faecalis. We show that ClpE-ClpP forms an autonomous and efficient protease, which degrades misfolded and aggregated model substrates and the stress-responsive transcriptional regulator CtsR. This qualifies ClpE-ClpP as a central component of bacterial protein quality control systems and explains formerly reported stress-sensitive phenotypes of clpE mutants. ClpE substrate specificity is mediated by its N-terminal domain, which is crucial for targeting misfolded and aggregated proteins. ClpE assembles into a tetrahedral structure formed by four hexamers that interact via their coiled-coil M-domains. ClpP binding to ClpE tetrahedrons triggers the formation of large clusters of proteolytic complexes in vitro and in vivo. Such assembly in principle can allow for spatially confined proteolysis, separating the proteolytic activity of ClpE-ClpP complexes from other cellular processes. Indeed, ClpE M-domain mutants, which are deficient in cluster formation, exhibit increased toxicity in vivo.
History
DepositionMar 11, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57170.png

Downloads & links

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Map

FileDownload / File: emd_57170.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.063
Minimum - Maximum-0.1907493 - 0.47060972
Average (Standard dev.)-0.0004014345 (±0.014224146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57170_msk_1.map
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Additional map: #1

Fileemd_57170_additional_1.map
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Half map: #1

Fileemd_57170_half_map_1.map
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Half map: #2

Fileemd_57170_half_map_2.map
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Sample components

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Entire : E. faecalis AAA+ protease ClpE/ClpP complex

EntireName: E. faecalis AAA+ protease ClpE/ClpP complex
Components
  • Complex: E. faecalis AAA+ protease ClpE/ClpP complex
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: unknown substrate bound to ClpE/ClpP
    • Protein or peptide: ATP-dependent Clp protease, ATP-binding subunit ClpE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: E. faecalis AAA+ protease ClpE/ClpP complex

SupramoleculeName: E. faecalis AAA+ protease ClpE/ClpP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Enterobacter (bacteria)

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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: Enterobacter (bacteria)
Molecular weightTheoretical: 21.640496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLIPTVIEQ SSRGERAYDI YSRLLKDRII MLSGPIDDNV ANSVIAQLLF LDAQDSEKDI YLYINSPGGS VSAGLAIFDT MNFVKADVQ TIVLGMAASM GSFLLTAGQK GKRFALPNAE IMIHQPLGGA QGQATEIEIA ARHILDTRQR LNSILAERTG Q PIEVIERD ...String:
MNLIPTVIEQ SSRGERAYDI YSRLLKDRII MLSGPIDDNV ANSVIAQLLF LDAQDSEKDI YLYINSPGGS VSAGLAIFDT MNFVKADVQ TIVLGMAASM GSFLLTAGQK GKRFALPNAE IMIHQPLGGA QGQATEIEIA ARHILDTRQR LNSILAERTG Q PIEVIERD TDRDNYMTAE QAKEYGLIDE VMENSSALN

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #2: unknown substrate bound to ClpE/ClpP

MacromoleculeName: unknown substrate bound to ClpE/ClpP / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacter (bacteria)
Molecular weightTheoretical: 1.379692 KDa
SequenceString:
(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 ClpE

MacromoleculeName: ATP-dependent Clp protease, ATP-binding subunit ClpE / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Enterobacter (bacteria)
Molecular weightTheoretical: 82.589953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MICQNCQQNE ATIHLYANVN GQRKQLDYCQ SCYQKLKNQA NNSPQNMGQD PFGFGSLDDL YRSLSRQMQQ GNPYEQQTPP TQFGDGGNG GQPPRGGAGA GQGLLGEYGI NITEAARQGD IDPVVGRDQE IKRVIEILNR RTKNNPVLIG EPGVGKTAVV E GLAQKIVD ...String:
MICQNCQQNE ATIHLYANVN GQRKQLDYCQ SCYQKLKNQA NNSPQNMGQD PFGFGSLDDL YRSLSRQMQQ GNPYEQQTPP TQFGDGGNG GQPPRGGAGA GQGLLGEYGI NITEAARQGD IDPVVGRDQE IKRVIEILNR RTKNNPVLIG EPGVGKTAVV E GLAQKIVD GDVPQKLLDK EVIRLDVVSL VQGTGIRGQF EERMQKLIEE ITEAENVILF IDEVHEIVGA GAAGDGNMDA GN ILKPALA RGELQLVGAT TLNEYRIIEK DAALERRMQP VQVDEPTVAE TITILHGLQK RYEDYHHVKY TDEAINAAAN LSN RYIQDR FLPDKAIDLL DESGSKMNLT IQLVDPKTID KKLAEAEQQK QQASAEEDFE KAAYYRDQIN KLQAMKEKQI SDEE TPVIT EKDIEAIVEQ KTGIPVGDLK EKEQTQLKNL AVDLKAHVVG QDDAVDKVAK AIRRNRVGLG KQNRPIGSFL FVGPT GVGK TELAKQLAFE LFGSEDSMVR FDMSEYMEKH SVSKLIGSPP GYVGYDEAGQ LTEKVRRNPY SLILLDEVEK AHPDVL HMF LQILDDGRLT DAQGRTVSFK DTIIIMTSNA GTGAVEANVG FGAAREGVTK SVLGQLNNFF TPEFLNRFDG IIEFKAL SK ENLMNIVSLM LEEVNSLLAK QKLHIEVPTE VKEKLVDLGY DPAMGARPLR RTIQEQIEDG IAEYYLDHPE NHQLVAAL D NEGKIIVTGA QEVTKTETST SDQAE

UniProtKB: ATP-dependent Clp protease, ATP-binding subunit ClpE

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 10 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 2.2 µm / Nominal defocus min: 0.3 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 556680
Initial angle assignmentType: OTHER / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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