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- EMDB-72339: Human mitochondrial ClpP V62A variant -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72339
TitleHuman mitochondrial ClpP V62A variant
Map dataUnsharpened map
Sample
  • Complex: Human mitochondrial ClpP V62A mutant
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsProtease / Proteolysis / HYDROLASE / Mutant
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / 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: 3.2 Å
AuthorsUday AB / Zeytuni N / Goncalves M / Vahidi S
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-191940 Canada
CitationJournal: Nat Commun / Year: 2026
Title: Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site
Authors: Goncalves MM / Uday AB / Watson IDG / Chau AM / Kalhor-Monfared S / Wan B / Kiyota T / Currie SQW / Jitkova Y / Feng Y / Diamandas M / Ling D / Ma M / Mancini RS / Wang Z / Casas-Selves M / ...Authors: Goncalves MM / Uday AB / Watson IDG / Chau AM / Kalhor-Monfared S / Wan B / Kiyota T / Currie SQW / Jitkova Y / Feng Y / Diamandas M / Ling D / Ma M / Mancini RS / Wang Z / Casas-Selves M / Joshi D / Mohammed M / Subramaniam R / Fernandes EL / Yan Y / Pomroy N / Hurren R / Gronda M / Velyvis A / Yudin AK / Reed MA / Prive G / Aman A / Isaac M / Marcellus R / Uehling D / Schimmer AD / Zeytuni N / Vahidi S
History
DepositionAug 26, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72339.png

Downloads & links

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Map

FileDownload / File: emd_72339.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 384 pix.
= 259.2 Å		0.68 Å/pix.
x 384 pix.
= 259.2 Å		0.68 Å/pix.
x 384 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0277
Minimum - Maximum-0.05518108 - 0.13106194
Average (Standard dev.)-0.0000020663297 (±0.0041123405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72339_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map used for refinement

Fileemd_72339_additional_1.map
AnnotationSharpened map used for refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_72339_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_72339_half_map_2.map
AnnotationHalf-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 mitochondrial ClpP V62A mutant

EntireName: Human mitochondrial ClpP V62A mutant
Components
  • Complex: Human mitochondrial ClpP V62A mutant
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit, mitochondrial

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Supramolecule #1: Human mitochondrial ClpP V62A mutant

SupramoleculeName: Human mitochondrial ClpP V62A mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 7 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.151822 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SLIPIAVEQT GRGERAYDIY SRLLRERIVC VMGPIDDSVA SLVIAQLLFL QSESNKKPIH MYINSPGGVV TAGLAIYDTM QYILNPICT WCVGQAASMG SLLLAAGTPG MRHSLPNSRI MIHQPSGGAR GQATDIAIQA EEIMKLKKQL YNIYAKHTKQ S LQVIESAM ...String:
SLIPIAVEQT GRGERAYDIY SRLLRERIVC VMGPIDDSVA SLVIAQLLFL QSESNKKPIH MYINSPGGVV TAGLAIYDTM QYILNPICT WCVGQAASMG SLLLAAGTPG MRHSLPNSRI MIHQPSGGAR GQATDIAIQA EEIMKLKKQL YNIYAKHTKQ S LQVIESAM ERDRYMSPME AQEFGILDKV LVHPPQDGED EPTLVQKEPV EAAPAAEPVP AST

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

Concentration21 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
100.0 mMKClPottassium chloride
10.0 mMMgCl2Magnesium chloride
1.0 mMC4H10O2S2Dithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio model generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 360193
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Homogenous refinement in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement in cryoSPARC
FSC plot (resolution estimation)

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