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- EMDB-71599: hClpP with DM -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71599
TitlehClpP with DM
Map data
Sample
  • Complex: Human mitochondrial ClpP in complex with Bortezomib
KeywordsMitochondrial protein / serine protease / structural protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsChen W / Yang J / Lander GC
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
DepositionJul 4, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71599.png

Downloads & links

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Map

FileDownload / File: emd_71599.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 300 pix.
= 282. Å		0.94 Å/pix.
x 300 pix.
= 282. Å		0.94 Å/pix.
x 300 pix.
= 282. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.639
Minimum - Maximum-3.2444112 - 3.806113
Average (Standard dev.)-0.00031374246 (±0.100854054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 282.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71599_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71599_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71599_half_map_2.map
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 in complex with Bortezomib

EntireName: Human mitochondrial ClpP in complex with Bortezomib
Components
  • Complex: Human mitochondrial ClpP in complex with Bortezomib

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Supramolecule #1: Human mitochondrial ClpP in complex with Bortezomib

SupramoleculeName: Human mitochondrial ClpP in complex with Bortezomib / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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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

Concentration15 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
150.0 mMsodium chlorideNaCl
5.0 %glycerol
2.0 mMDithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
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: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3972 / Average exposure time: 7.0 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: 53191 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2800000000000002 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 150000
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: 1924070
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1tg6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 514935
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)

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Atomic model buiding 1

Initial modelPDB ID:

1tg6


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.8.9.1)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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