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- PDB-29hb: Cryo-EM structure of the ClpE/ClpP degradation complex from E.faecalis -

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Basic information

Entry
Database: PDB / ID: 29hb
TitleCryo-EM structure of the ClpE/ClpP degradation complex from E.faecalis
Components
  • ATP-dependent Clp protease proteolytic subunit
  • ATP-dependent Clp protease, ATP-binding subunit ClpE
  • unknown substrate bound to ClpE/ClpP
KeywordsCHAPERONE / AAA+ chaperone / protease
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
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease, ATP-binding subunit ClpE
Similarity search - Component
Biological speciesEnterobacter (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCarroni, M. / Mogk, A.
Funding support Sweden, 2items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: unknown substrate bound to ClpE/ClpP
I: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease, ATP-binding subunit ClpE
c: ATP-dependent Clp protease, ATP-binding subunit ClpE
d: ATP-dependent Clp protease, ATP-binding subunit ClpE
a: ATP-dependent Clp protease, ATP-binding subunit ClpE
e: ATP-dependent Clp protease, ATP-binding subunit ClpE
f: ATP-dependent Clp protease, ATP-binding subunit ClpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)804,95831
Polymers799,88621
Non-polymers5,07210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 21640.496 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter (bacteria) / Gene: clpP, EF_0771 / Production host: Escherichia coli (E. coli) / References: UniProt: Q837R0, endopeptidase Clp
#2: Protein/peptide unknown substrate bound to ClpE/ClpP


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacter (bacteria)
#3: Protein
ATP-dependent Clp protease, ATP-binding subunit ClpE


Mass: 82589.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter (bacteria) / Gene: clpE, EF_0706 / Production host: Escherichia coli (E. coli) / References: UniProt: Q837W9
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. faecalis AAA+ protease ClpE/ClpP complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Enterobacter (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556680 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00246786
ELECTRON MICROSCOPYf_angle_d0.48863267
ELECTRON MICROSCOPYf_dihedral_angle_d7.4386723
ELECTRON MICROSCOPYf_chiral_restr0.0397354
ELECTRON MICROSCOPYf_plane_restr0.0038285

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