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- EMDB-47232: Human ClpX-bound ClpP -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47232
TitleHuman ClpX-bound ClpP
Map datahClpX-bound hClpP sharpened map
Sample
  • Complex: Human ClpX-bound ClpP
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsMitochondrial protein / serine protease / structural protein
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChen WC
Funding support United States, 3 items
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 WC
History
DepositionOct 8, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47232.png

Downloads & links

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Map

FileDownload / File: emd_47232.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhClpX-bound hClpP sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 352 pix.
= 320.32 Å		0.91 Å/pix.
x 352 pix.
= 320.32 Å		0.91 Å/pix.
x 352 pix.
= 320.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.9528086 - 4.6568007
Average (Standard dev.)0.00061895006 (±0.117180936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 320.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: hClpX-bound hClpP half map A

Fileemd_47232_half_map_1.map
AnnotationhClpX-bound hClpP half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hClpX-bound hClpP half map B

Fileemd_47232_half_map_2.map
AnnotationhClpX-bound hClpP half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 Clp protease proteolytic subunit, mitochondrial

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Supramolecule #1: Human ClpX-bound ClpP

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

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Macromolecule #1: ATP-dependent Clp protease proteolytic subunit, mitochondrial

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.217752 KDa
Recombinant expressionOrganism: Escherichia coli 0.1197 (bacteria)
SequenceString: LIPIVVEQTG RGERAYDIYS RLLRERIVCV MGPIDDSVAS LVIAQLLFLQ SESNKKPIHM YINSPGGVVT AGLAIYDTMQ YILNPICTW CVGQAAAMGS LLLAAGTPGM RHSLPNSRIM IHQPSGGARG QATDIAIQAE EIMKLKKQLY NIYAKHTKQS L QVIESAME ...String:
LIPIVVEQTG RGERAYDIYS RLLRERIVCV MGPIDDSVAS LVIAQLLFLQ SESNKKPIHM YINSPGGVVT AGLAIYDTMQ YILNPICTW CVGQAAAMGS LLLAAGTPGM RHSLPNSRIM IHQPSGGARG QATDIAIQAE EIMKLKKQLY NIYAKHTKQS L QVIESAME RDRYMSPMEA QEFGILDKVL VHPP

UniProtKB: ATP-dependent Clp protease proteolytic subunit, mitochondrial

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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 R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
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
SoftwareName: Leginon
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: 10333 / 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 correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bba

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 1315867
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bba


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.8.9.2)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9dw0:
Human ClpX-bound ClpP

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