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- EMDB-71425: Human ClpX initial assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-71425
TitleHuman ClpX initial assembly
Map data
Sample
  • Complex: Human ClpX-bound ClpP
    • Protein or peptide: ATP-dependent clpX-like chaperone, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMitochondrial protein / serine protease / structural protein / HYDROLASE
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
ATP-dependent clpX-like chaperone, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsChen WC
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71425.png

Downloads & links

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Map

FileDownload / File: emd_71425.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 144 pix.
= 165.6 Å		1.15 Å/pix.
x 144 pix.
= 165.6 Å		1.15 Å/pix.
x 144 pix.
= 165.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.208
Minimum - Maximum-0.38503984 - 0.87530416
Average (Standard dev.)0.018953891 (±0.069179095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 165.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71425_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_71425_half_map_1.map
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Half map: #1

Fileemd_71425_half_map_2.map
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Sample components

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Entire : Human ClpX-bound ClpP

EntireName: Human ClpX-bound ClpP
Components
  • Complex: Human ClpX-bound ClpP
    • Protein or peptide: ATP-dependent clpX-like chaperone, mitochondrial
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human ClpX-bound ClpP

SupramoleculeName: Human ClpX-bound ClpP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: ATP-dependent clpX-like chaperone, mitochondrial

MacromoleculeName: ATP-dependent clpX-like chaperone, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.56798 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FTETPAYFAS KDGISKDGSG DGNKKSASEG SSKKSGSGNS GKGGNQLRCP KCGDLCTHVE TFVSSTRFVK CEKCHHFFVV LSEADSKKS IIKEPESAAE AVKLAFQQKP PPPPKKIYNY LDKYVVGQSF AKKVLSVAVY NHYKRIYNNI PANLRQQAEV E KQTSLTPR ...String:
FTETPAYFAS KDGISKDGSG DGNKKSASEG SSKKSGSGNS GKGGNQLRCP KCGDLCTHVE TFVSSTRFVK CEKCHHFFVV LSEADSKKS IIKEPESAAE AVKLAFQQKP PPPPKKIYNY LDKYVVGQSF AKKVLSVAVY NHYKRIYNNI PANLRQQAEV E KQTSLTPR ELEIRRREDE YRFTKLLQIA GISPHGNALG ASMQQQVNQQ IPQEKRGGEV LDSSHDDIKL EKSNILLLGP TG SGKTLLA QTLAKCLDVP FAICDCTTLT QAGYVGEDIE SVIAKLLQDA NYNVEKAQQG IVFLDQVDKI GSVPGIHQLR DVG GEGVQQ GLLKLLEGTI VNVPEKNSRK LRGETVQVDT TNILFVASGA FNGLDRIISR RKNEKYLGFG TPSNLGKGRR AAAA ADLAN RSGESNTHQD IEEKDRLLRH VEARDLIEFG MIPEFVGRLP VVVPLHSLDE KTLVQILTEP RNAVIPQYQA LFSMD KCEL NVTEDALKAI ARLALERKTG ARGLRSIMEK LLLEPMFEVP NSDIVCVEVD KEVVEGKKEP GYIRAPTKES SEEEYD SGV EEEGWPRQAD AANS

UniProtKB: ATP-dependent clpX-like chaperone, mitochondrial

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMsodium chlorideNaCl
5.0 %glycerol
2.0 mMmagnesium chlorideMgCl2
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber 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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 3298 / Average exposure time: 6.8 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 54945 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 0.23 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1940578
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9dvy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 26410
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

9dvy


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9p9v:
Human ClpX initial assembly

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