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- EMDB-73977: Masked Classification of Prohibitin Complexes Showing the Prohibi... -

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Basic information

Entry
Database: EMDB / ID: EMD-73977
TitleMasked Classification of Prohibitin Complexes Showing the Prohibitin complex without an Additional Matrix-Facing Density (Class 2)
Map dataRELION auto-refine result for the prohibitin complex, class 2, showing no density on the matrix side of the inner mitochondrial membrane
Sample
  • Complex: Prohibitin complex from mouse embryonic fibroblasts
KeywordsProhibitin complex / mitochondria / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsMedina M / Rahmani H / Chang Y / Barad BA / Grotjahn DA
Funding support United States, 7 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRR-65-21 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RF1NS125674 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
Other privatePew Charitable Trusts
Other privateARCS (Achievement rewards for college scientists)
Other privateCollins Medical Trust
Other privateThe Bachrach Family Foundation
CitationJournal: bioRxiv / Year: 2025
Title: Prohibitin complexes associate with unique membrane microdomains in cells
Authors: Medina M / Rahmani H / Chang Y / Barad BA / Grotjahn DA
History
DepositionNov 20, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73977.png

Downloads & links

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Map

FileDownload / File: emd_73977.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION auto-refine result for the prohibitin complex, class 2, showing no density on the matrix side of the inner mitochondrial membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 128 pix.
= 425.6 Å		3.33 Å/pix.
x 128 pix.
= 425.6 Å		3.33 Å/pix.
x 128 pix.
= 425.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.74066806 - 1.1174662
Average (Standard dev.)0.033918913 (±0.21747135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 425.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map1 of the relion auto-refine

Fileemd_73977_half_map_1.map
AnnotationHalf-map1 of the relion auto-refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map2 of the relion auto-refine

Fileemd_73977_half_map_2.map
AnnotationHalf-map2 of the relion auto-refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prohibitin complex from mouse embryonic fibroblasts

EntireName: Prohibitin complex from mouse embryonic fibroblasts
Components
  • Complex: Prohibitin complex from mouse embryonic fibroblasts

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Supramolecule #1: Prohibitin complex from mouse embryonic fibroblasts

SupramoleculeName: Prohibitin complex from mouse embryonic fibroblasts / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: Quantifoil R1/4 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 310.15 K / Instrument: FEI VITROBOT MARK IV
DetailsCells were frozen and then thinned using Aquilos2 for FIB-milling

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 415
ExtractionNumber tomograms: 27 / Number images used: 415 / Method: Manual picking / Software - Name: I3 / Software - details: Manual dipole selection
CTF correctionSoftware - Name: Warp (ver. 1.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 2 / Software - Name: I3
Details: Classification was done in I3 using principal component analysis on bin6 tomogram (9.98A/pixel) and the resulting particles were extracted at 3.325A/pixel in Warp and refined in relion.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Software - details: Relion
FSC plot (resolution estimation)

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