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- PDB-9ndj: Cryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex fro... -

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Basic information

Entry
Database: PDB / ID: 9ndj
TitleCryo-EM structure of the endogenous ClpP1/ClpP2 heterocomplex from Pseudomonas aeruginosa bound to the AAA+ ClpX unfoldase.
Components
  • (ATP-dependent Clp protease proteolytic ...) x 2
  • ATP-dependent Clp protease ATP-binding subunit ClpX
  • Unknown substrate
KeywordsCHAPERONE / ClpXP / full-engaged state / AAA protease
Function / homology
Function and homology information


HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / : / ATP-dependent protein folding chaperone / : / ATPase binding / protein dimerization activity ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / : / ATP-dependent protein folding chaperone / : / ATPase binding / protein dimerization activity / serine-type endopeptidase activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / : / Clp protease, ATP-binding subunit ClpX / ClpX zinc binding (ZB) domain profile. / : / ClpP, Ser active site ...Zinc finger, ClpX C4-type superfamily / ClpX C4-type zinc finger / Zinc finger, ClpX C4-type / Clp protease, ATP-binding subunit ClpX, bacteria / ClpX C4-type zinc finger / : / Clp protease, ATP-binding subunit ClpX / ClpX zinc binding (ZB) domain profile. / : / 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 / 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, 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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit ClpX / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsGhanbarpour, A. / Zhang, J.J. / Baker, T.A. / Davis, J.H. / Sauer, R.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01-GM144542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
CitationJournal: Protein Sci / Year: 2025
Title: Structural insights into the Pseudomonas aeruginosa ClpP1•ClpP2 heterocomplex and its interactions with the AAA+ ClpX unfoldase.
Authors: Alireza Ghanbarpour / Jia Jia Zhang / Joseph H Davis / Tania A Baker / Robert T Sauer /
Abstract: ClpXP and other AAA+ proteases play central roles in bacterial proteostasis by degrading misfolded and regulatory proteins. In Pseudomonas aeruginosa, ClpXP consists of the ClpX unfoldase and ClpP ...ClpXP and other AAA+ proteases play central roles in bacterial proteostasis by degrading misfolded and regulatory proteins. In Pseudomonas aeruginosa, ClpXP consists of the ClpX unfoldase and ClpP peptidase, which influence critical adaptive processes contributing to stress resistance. P. aeruginosa ClpP1 and ClpP2 paralogs assemble into homomeric (ClpP1•ClpP1) and heteromeric (ClpP1•ClpP2) complexes. ClpP2 is only active in the ClpP1•ClpP2 heterocomplex. Here, we present a cryo-EM structure of ClpX•ClpP1•ClpP2, revealing how ClpX binds ClpP1, which in turn interacts with ClpP2. Comparison of the active heterocomplex with an inactive ClpP2 crystal structure shows that ClpP1 binding induces conformational changes in ClpP2, stabilizing an active catalytic triad. Differences in ClpP1 and ClpP2 substrate-binding residues and an unstructured ClpP2 N-terminal segment that protrudes into the peptidase chamber likely contribute to distinct peptide-cleavage specificities of ClpX•ClpP1•ClpP2 and ClpX•ClpP1•ClpP1. Given the role of ClpP1•ClpP2 in biofilm formation and virulence, these structural insights may provide a foundation for developing selective inhibitors to combat P. aeruginosa infections.
History
DepositionFeb 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: ATP-dependent Clp protease ATP-binding subunit ClpX
A: ATP-dependent Clp protease ATP-binding subunit ClpX
B: ATP-dependent Clp protease ATP-binding subunit ClpX
C: ATP-dependent Clp protease ATP-binding subunit ClpX
D: ATP-dependent Clp protease ATP-binding subunit ClpX
E: ATP-dependent Clp protease ATP-binding subunit ClpX
G: Unknown substrate
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: 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
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)612,64533
Polymers609,61621
Non-polymers3,02912
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

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ATP-dependent Clp protease proteolytic ... , 2 types, 14 molecules HIJKLMNPQRSTUV

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


Mass: 23529.143 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: clpP_4, clpP, ALP65_02974, CAZ10_25705, GNQ48_00520, GUL26_19790, IPC1295_05810, PAERUG_P19_London_7_VIM_2_05_10_05994
Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A072ZHR6, endopeptidase Clp
#4: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 23167.191 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: clpP, ALP65_00001 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A3M5ER03, endopeptidase Clp

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Protein / Protein/peptide , 2 types, 7 molecules FABCDEG

#1: Protein
ATP-dependent Clp protease ATP-binding subunit ClpX


Mass: 47049.688 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: clpX, ALP65_100029 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3M5DFV1
#2: Protein/peptide Unknown substrate


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 12 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

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: ClpX / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: 1750 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 52.67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7cryoSPARC4.4.1model fitting
9PHENIX1.14_3260:model refinement
CTF correctionDetails: Patch CTF estimation, cryoSPARC / Type: NONE
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135056 / Symmetry type: POINT

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