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- EMDB-73107: Uncrosslinked hClpXP composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-73107
TitleUncrosslinked hClpXP composite map
Map dataunxlinked-hClpXP-composite-map
Sample
  • Complex: hClpXP
KeywordsMitochondrial AAA+ ATPase / mitochondrial protease / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsChen W
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/Office of the DirectorS10 0D032467 United States
National Institutes of Health/Office of the DirectorNS095892 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
DepositionOct 10, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73107.png

Downloads & links

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Map

FileDownload / File: emd_73107.map.gz / Format: CCP4 / Size: 52 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunxlinked-hClpXP-composite-map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 237 pix.
= 272.55 Å		1.15 Å/pix.
x 233 pix.
= 267.95 Å		1.15 Å/pix.
x 247 pix.
= 284.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.09798191 - 1.6205267
Average (Standard dev.)0.023125676 (±0.061138436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-34-40-75
Dimensions233247237
Spacing247233237
CellA: 284.05 Å / B: 267.94998 Å / C: 272.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : hClpXP

EntireName: hClpXP
Components
  • Complex: hClpXP

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Supramolecule #1: hClpXP

SupramoleculeName: hClpXP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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: 4500
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

71595

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 46168
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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