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- EMDB-55207: Subtomogram average of the mtHsp60:mtHsp10 Football complex from HeLa -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-55207
TitleSubtomogram average of the mtHsp60:mtHsp10 Football complex from HeLa
Map dataCombined FSC-filtered map
Sample
  • Cell: HeLa
KeywordsMitochondria / human / HeLa / folding / Chaperonin / CHAPERONE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 7.76 Å
AuthorsEhses K / Fernandez-Busnadiego R
Funding support Germany, United States, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)448415290 Germany
Michael J. Fox FoundationMJFF-010458 United States
Aligning Science Across Parkinsons (ASAP)ASAP-000282 United States
German Research Foundation (DFG)EXC 2067 Germany
CitationJournal: To Be Published
Title: Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress
Authors: Ehses K / Lopez-Alonso JP / Antico O / Abdussalam A / Muqit MMK / Ubarretxena-Belandia I / Fernandez-Busnadiego R
History
DepositionSep 26, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55207.png

Downloads & links

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Map

FileDownload / File: emd_55207.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined FSC-filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.31 Å/pix.
x 216 pix.
= 499.478 Å		2.31 Å/pix.
x 216 pix.
= 499.478 Å		2.31 Å/pix.
x 216 pix.
= 499.478 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00183
Minimum - Maximum-0.002810429 - 0.0074203676
Average (Standard dev.)-0.000019402249 (±0.00026602068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 499.47842 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Unfiltered Halfset 1 map

Fileemd_55207_half_map_1.map
AnnotationUnfiltered Halfset 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered Halfset 2 map

Fileemd_55207_half_map_2.map
AnnotationUnfiltered Halfset 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 : HeLa

EntireName: HeLa
Components
  • Cell: HeLa

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Supramolecule #1: HeLa

SupramoleculeName: HeLa / type: cell / ID: 1 / Parent: 0 / Details: PINK1-GFP Knockin
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
Details: Addition of 10% Glycerol immediately before plunging into the medium for improved vitrification.
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV / Details: Backside blotting.
DetailsCells directly grown on EM grids

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 4.0 e/Å2
Details: For subtomogram averaging, only the first 20 frames were used. The total dose per tilt-series equals 150e/A2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 7.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Software - details: Reconstruction by M / Number subtomograms used: 22338
ExtractionNumber tomograms: 242 / Number images used: 145200
Software:
Namedetails
DynamoFor template matching
MATLABFor extraction and parsing

Details: Initial extract carried out with Dynamo template-matching. Then, another round of extraction was performed using Deepfinder.
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Software:
Namedetails
RELION (ver. 4.0)Final 3D refinement before M
WarpPose optimization in M

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