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- EMDB-12354: ordered protein arrays on the outer mitochondrial membrane of mou... -

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Basic information

Entry
Database: EMDB / ID: EMD-12354
Titleordered protein arrays on the outer mitochondrial membrane of mouse sperm mitochondria
Map datasubtomogram average of ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria
Sample
  • Cell: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 24.0 Å
AuthorsLeung MR / Zeev-Ben-Mordehai T
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.007 Netherlands
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: In-cell structures of conserved supramolecular protein arrays at the mitochondria-cytoskeleton interface in mammalian sperm.
Authors: Miguel Ricardo Leung / Riccardo Zenezini Chiozzi / Marc C Roelofs / Johannes F Hevler / Ravi Teja Ravi / Paula Maitan / Min Zhang / Heiko Henning / Elizabeth G Bromfield / Stuart C Howes / ...Authors: Miguel Ricardo Leung / Riccardo Zenezini Chiozzi / Marc C Roelofs / Johannes F Hevler / Ravi Teja Ravi / Paula Maitan / Min Zhang / Heiko Henning / Elizabeth G Bromfield / Stuart C Howes / Bart M Gadella / Albert J R Heck / Tzviya Zeev-Ben-Mordehai /
Abstract: Mitochondria-cytoskeleton interactions modulate cellular physiology by regulating mitochondrial transport, positioning, and immobilization. However, there is very little structural information ...Mitochondria-cytoskeleton interactions modulate cellular physiology by regulating mitochondrial transport, positioning, and immobilization. However, there is very little structural information defining mitochondria-cytoskeleton interfaces in any cell type. Here, we use cryofocused ion beam milling-enabled cryoelectron tomography to image mammalian sperm, where mitochondria wrap around the flagellar cytoskeleton. We find that mitochondria are tethered to their neighbors through intermitochondrial linkers and are anchored to the cytoskeleton through ordered arrays on the outer mitochondrial membrane. We use subtomogram averaging to resolve in-cell structures of these arrays from three mammalian species, revealing they are conserved across species despite variations in mitochondrial dimensions and cristae organization. We find that the arrays consist of boat-shaped particles anchored on a network of membrane pores whose arrangement and dimensions are consistent with voltage-dependent anion channels. Proteomics and in-cell cross-linking mass spectrometry suggest that the conserved arrays are composed of glycerol kinase-like proteins. Ordered supramolecular assemblies may serve to stabilize similar contact sites in other cell types in which mitochondria need to be immobilized in specific subcellular environments, such as in muscles and neurons.
History
DepositionFeb 12, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12354.png

Downloads & links

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Map

FileDownload / File: emd_12354.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria
Voxel sizeX=Y=Z: 5.66 Å
Density
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-134.68938 - 153.54594
Average (Standard dev.)-21.319489 (±28.305473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408080
Spacing804080
CellA: 452.8 Å / B: 226.4 Å / C: 452.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.665.665.66
M x/y/z804080
origin x/y/z0.0000.0000.000
length x/y/z452.800226.400452.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS804080
D min/max/mean-134.689153.546-21.319

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Supplemental data

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Sample components

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Entire : ordered protein arrays on the axoneme-facing surface of the outer...

EntireName: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria
Components
  • Cell: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria

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Supramolecule #1: ordered protein arrays on the axoneme-facing surface of the outer...

SupramoleculeName: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in mouse sperm mitochondria
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6 / Tissue: sperm

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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: 7.5
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Detailslamellae prepared by cryo-focused ion beam milling of mouse epididymal sperm

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 8 / Number images used: 1944 / Reference model: random particle from the dataset / Software - Name: PEET (ver. 1.13.0)
CTF correctionSoftware - Name: IMOD (ver. 4.10.25)
Final 3D classificationNumber classes: 1
Final angle assignmentType: OTHER / Software - Name: PEET (ver. 1.13.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.13.0) / Number subtomograms used: 1944

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