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- PDB-9dvy: Human mitochondrial ClpX with endogenous substrate -

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Basic information

Entry
Database: PDB / ID: 9dvy
TitleHuman mitochondrial ClpX with endogenous substrate
Components
  • ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
  • Unidentified endogenous substrate
KeywordsSTRUCTURAL PROTEIN / Mitochondrial protein / AAA+ ATPase
Function / homology
Function and homology information


mitochondrial endopeptidase Clp complex / endopeptidase Clp complex / peptidase activator activity / non-chaperonin molecular chaperone ATPase / mitochondrial nucleoid / ATP metabolic process / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding ...mitochondrial endopeptidase Clp complex / endopeptidase Clp complex / peptidase activator activity / non-chaperonin molecular chaperone ATPase / mitochondrial nucleoid / ATP metabolic process / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / unfolded protein binding / mitochondrial inner membrane / protein dimerization activity / mitochondrial matrix / ATP hydrolysis activity / mitochondrion / proteolysis / zinc ion binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / 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 ...Clp protease, ATP-binding subunit ClpX / Zinc finger, ClpX C4-type / 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 / ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent clpX-like chaperone, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen, W.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD032467 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095892 United States
CitationJournal: To Be Published
Title: Assembly and proteolytic activation human ClpXP defined by cryo-EM
Authors: Chen, W.C. / Yang, J. / Lander, G.C.
History
DepositionOct 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data 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 ATP-binding subunit clpX-like, mitochondrial
B: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
C: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
D: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
E: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
F: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
G: Unidentified endogenous substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,67616
Polymers312,1227
Non-polymers2,5539
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 Clp protease ATP-binding subunit clpX-like, mitochondrial


Mass: 51847.184 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
#2: Protein/peptide Unidentified endogenous substrate


Mass: 1039.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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 hexamer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.31 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
32 mMmagnesium chlorideMgCl21
45 %glycerol1
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: 2.7 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: 10333
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 50

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
4cryoSPARC4.3CTF correction
7Coot0.8.9.1model fitting
9cryoSPARC4.3initial Euler assignment
10cryoSPARC4.3final Euler assignment
11cryoSPARC4.3classification
12cryoSPARC4.33D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1940578
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 513188 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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