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- PDB-9p9v: Human ClpX initial assembly -

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Basic information

Entry
Database: PDB / ID: 9p9v
TitleHuman ClpX initial assembly
ComponentsATP-dependent clpX-like chaperone, mitochondrial
KeywordsHYDROLASE / Mitochondrial protein / serine protease / structural protein
Function / homology
Function and homology information


mitochondrial endopeptidase Clp complex / endopeptidase Clp complex / perinuclear theca / peptidase activator activity / non-chaperonin molecular chaperone ATPase / mitochondrial nucleoid / ATP metabolic process / Mitochondrial protein degradation / : / ATP-dependent protein folding chaperone ...mitochondrial endopeptidase Clp complex / endopeptidase Clp complex / perinuclear theca / peptidase activator activity / non-chaperonin molecular chaperone ATPase / mitochondrial nucleoid / ATP metabolic process / Mitochondrial protein degradation / : / ATP-dependent protein folding chaperone / unfolded protein binding / protein dimerization activity / mitochondrial inner membrane / mitochondrial matrix / ATP hydrolysis activity / mitochondrion / proteolysis / zinc ion binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
: / CLPX-like, zinc ribbon domain / : / Clp protease, ATP-binding subunit ClpX / ClpX zinc binding (ZB) domain profile. / : / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) ...: / CLPX-like, zinc ribbon domain / : / Clp protease, ATP-binding subunit ClpX / ClpX zinc binding (ZB) domain profile. / : / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / ATP-dependent clpX-like chaperone, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsChen, W.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/Office of the DirectorS10 OD032467 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095892 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.
Authors: Wenqian Chen / Gabriel C Lander / Jie Yang /
Abstract: The human ClpXP complex (hClpXP) orchestrates mitochondrial protein quality control through targeted degradation of misfolded and unnecessary proteins. While bacterial ClpXP systems are well ...The human ClpXP complex (hClpXP) orchestrates mitochondrial protein quality control through targeted degradation of misfolded and unnecessary proteins. While bacterial ClpXP systems are well characterized, the assembly and regulation of human ClpXP remain poorly understood. In this study, we elucidate the complete assembly pathway of hClpXP through high-resolution cryo-electron microscopy (cryo-EM) structures. Our findings confirm that hClpP exists as a single-ring heptamer in isolation and reveal a previously undocumented initial assembly complex in which hexameric hClpX first engages with heptameric hClpP. We further demonstrate how this interaction drives substantial conformational rearrangements that facilitate the formation of tetradecameric hClpP within the fully assembled complex. Notably, we characterize a unique eukaryotic sequence in hClpX, termed the E-loop, which plays a critical role in stabilizing hexamer assembly and maintaining ATPase activity. Additionally, we show that peptide binding at the hClpP active site triggers further structural changes essential for achieving full proteolytic competence. Together, these structures provide unprecedented mechanistic insights into the stepwise assembly and activation of hClpXP, significantly advancing our understanding of this essential mitochondrial protein degradation machinery.
History
DepositionJun 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: 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 clpX-like chaperone, mitochondrial
B: ATP-dependent clpX-like chaperone, mitochondrial
C: ATP-dependent clpX-like chaperone, mitochondrial
D: ATP-dependent clpX-like chaperone, mitochondrial
E: ATP-dependent clpX-like chaperone, mitochondrial
F: ATP-dependent clpX-like chaperone, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,97112
Polymers381,4086
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP-dependent clpX-like chaperone, mitochondrial / ATP-dependent Clp protease ATP-binding subunit clpX-like / mitochondrial / Caseinolytic ...ATP-dependent Clp protease ATP-binding subunit clpX-like / mitochondrial / Caseinolytic mitochondrial matrix peptidase chaperone subunit X


Mass: 63567.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPX / Production host: Escherichia coli (E. coli)
References: UniProt: O76031, non-chaperonin molecular chaperone ATPase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, 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: Human ClpX-bound ClpP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2150 mMsodium chlorideNaCl1
35 %glycerol1
42 mMmagnesium chlorideMgCl21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 90 %
Details: The sample was prepared using manual blot-and-plunge freezing method in cold room (4 celsius)

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 54945 X / Nominal defocus max: 3300 nm / Nominal defocus min: 230 nm / Cs: 3.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3298
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 50

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
12cryoSPARC4.7.03D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1940578
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26410 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9DVY

9dvy


Accession code: 9DVY / Source name: PDB / Type: experimental model

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