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- EMDB-47226: Human mitochondrial ClpX with endogenous substrate -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47226
TitleHuman mitochondrial ClpX with endogenous substrate
Map datahClpX sharpened map
Sample
  • Complex: Human ClpX hexamer
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
    • Protein or peptide: Unidentified endogenous substrate
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMitochondrial protein / AAA+ ATPase / STRUCTURAL PROTEIN
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 / protein dimerization activity / mitochondrial inner membrane / 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
ATP-dependent clpX-like chaperone, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 / Yang J / Lander GC
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_47226.png

Downloads & links

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Map

FileDownload / File: emd_47226.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhClpX 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: 0.273
Minimum - Maximum-1.7766943 - 3.599294
Average (Standard dev.)-0.0018820462 (±0.06210584)
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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Mask #1

Fileemd_47226_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hClpX half-map-B

Fileemd_47226_half_map_1.map
AnnotationhClpX half-map-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hClpX half-map-A

Fileemd_47226_half_map_2.map
AnnotationhClpX half-map-A
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 hexamer

EntireName: Human ClpX hexamer
Components
  • Complex: Human ClpX hexamer
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
    • Protein or peptide: Unidentified endogenous substrate
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human ClpX hexamer

SupramoleculeName: Human ClpX hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 310 KDa

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Macromolecule #1: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitocho...

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.847184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IIKEPESAAE AVKLAFQQKP PPPPKKIYNY LDKYVVGQSF AKKVLSVAVY NHYKRIYNNI PANLRQQAEV EKQTSLTPRE LEIRRREDE YRFTKLLQIA GISPHGNALG ASMQQQVNQQ IPQEKRGGEV LDSSHDDIKL EKSNILLLGP TGSGKTLLAQ T LAKCLDVP ...String:
IIKEPESAAE AVKLAFQQKP PPPPKKIYNY LDKYVVGQSF AKKVLSVAVY NHYKRIYNNI PANLRQQAEV EKQTSLTPRE LEIRRREDE YRFTKLLQIA GISPHGNALG ASMQQQVNQQ IPQEKRGGEV LDSSHDDIKL EKSNILLLGP TGSGKTLLAQ T LAKCLDVP FAICDCTTLT QAGYVGEDIE SVIAKLLQDA NYNVEKAQQG IVFLDQVDKI GSVPGIHQLR DVGGEGVQQG LL KLLEGTI VNVPEKNSRK LRGETVQVDT TNILFVASGA FNGLDRIISR RKNEKYLGFG TPSNLGKGRR AAAAADLANR SGE SNTHQD IEEKDRLLRH VEARDLIEFG MIPEFVGRLP VVVPLHSLDE KTLVQILTEP RNAVIPQYQA LFSMDKCELN VTED ALKAI ARLALERKTG ARGLRSIMEK LLLEPMFEVP NSDIVCVEVD KEVVEGKKEP GYIRAPTKES SE

UniProtKB: ATP-dependent clpX-like chaperone, mitochondrial

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Macromolecule #2: Unidentified endogenous substrate

MacromoleculeName: Unidentified endogenous substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.039273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / 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
2.0 mMmagnesium chlorideMgCl2
5.0 %glycerol
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
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: 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: 2.7 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 513188
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 modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.8.9.1)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9dvy:
Human mitochondrial ClpX with endogenous substrate

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