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Yorodumi- EMDB-12356: ordered protein arrays on the outer mitochondrial membrane of pig... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12356 | |||||||||
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Title | ordered protein arrays on the outer mitochondrial membrane of pig sperm mitochondria | |||||||||
Map data | subtomogram average of ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in pig sperm mitochondria | |||||||||
Sample |
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Biological species | Sus scrofa (pig) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 35.0 Å | |||||||||
Authors | Leung MR / Zeev-Ben-Mordehai T | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12356.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-12356-v30.xml emd-12356.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_12356.png | 147.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12356 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12356 | HTTPS FTP |
-Validation report
Summary document | emd_12356_validation.pdf.gz | 329.1 KB | Display | EMDB validaton report |
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Full document | emd_12356_full_validation.pdf.gz | 328.7 KB | Display | |
Data in XML | emd_12356_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_12356_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12356 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12356 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12356.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | subtomogram average of ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in pig sperm mitochondria | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ordered protein arrays on the axoneme-facing surface of the outer...
Entire | Name: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in pig sperm mitochondria |
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Components |
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-Supramolecule #1: ordered protein arrays on the axoneme-facing surface of the outer...
Supramolecule | Name: ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in pig sperm mitochondria type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: sperm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
Details | lamellae prepared by cryo-focused ion beam milling of pig sperm |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |