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Yorodumi- PDB-7nie: putative glycerol kinase-like proteins anchored on an array of vo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nie | ||||||
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Title | putative glycerol kinase-like proteins anchored on an array of voltage dependent anion channels in the outer mitochondrial membrane of pig sperm mitochondria | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / mitochondria / sperm | ||||||
Function / homology | Function and homology information Triglyceride biosynthesis / negative regulation of protein polymerization / voltage-gated monoatomic anion channel activity / glycerol-3-phosphate biosynthetic process / mitochondrial outer membrane permeabilization / glycerol kinase / phosphotransferase activity, alcohol group as acceptor / glycerol kinase activity / ceramide binding / glycerol metabolic process ...Triglyceride biosynthesis / negative regulation of protein polymerization / voltage-gated monoatomic anion channel activity / glycerol-3-phosphate biosynthetic process / mitochondrial outer membrane permeabilization / glycerol kinase / phosphotransferase activity, alcohol group as acceptor / glycerol kinase activity / ceramide binding / glycerol metabolic process / binding of sperm to zona pellucida / phosphatidylcholine binding / glycerol catabolic process / triglyceride metabolic process / cholesterol binding / porin activity / pore complex / mitochondrial nucleoid / negative regulation of intrinsic apoptotic signaling pathway / phosphorylation / acrosomal vesicle / mitochondrial outer membrane / mitochondrion Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å | ||||||
Authors | Leung, M.R. / Zeev-Ben-Mordehai, T. | ||||||
Funding support | Netherlands, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nie.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nie.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 7nie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nie_validation.pdf.gz | 770.4 KB | Display | wwPDB validaton report |
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Full document | 7nie_full_validation.pdf.gz | 826.4 KB | Display | |
Data in XML | 7nie_validation.xml.gz | 130.7 KB | Display | |
Data in CIF | 7nie_validation.cif.gz | 193.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/7nie ftp://data.pdbj.org/pub/pdb/validation_reports/ni/7nie | HTTPS FTP |
-Related structure data
Related structure data | 12357MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 53579.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) Plasmid details: lamellae prepared by cryo-focused ion beam milling of pig sperm Tissue: sperm / References: UniProt: A0A287BD08, glycerol kinase #2: Protein | Mass: 31637.484 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) Plasmid details: lamellae prepared by cryo-focused ion beam milling of pig sperm Tissue: sperm / References: UniProt: F1S2F6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: subtomogram average of ordered protein arrays on the axoneme-facing surface of the outer mitochondrial membrane in pig sperm mitochondria (alignment focused on one unit) Type: CELL / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) / Cellular location: midpiece / Organelle: mitochondria / Tissue: sperm |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 536 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 3 / Num. of volumes extracted: 268 / Reference model: random particle from the dataset | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: Homology models of pig glycerol kinase and VDAC2 were made using Robetta. Rigid body fitting was done with Chimera/ChimeraX. Putative GK proteins only fit in one orientation, but for VDAC ...Details: Homology models of pig glycerol kinase and VDAC2 were made using Robetta. Rigid body fitting was done with Chimera/ChimeraX. Putative GK proteins only fit in one orientation, but for VDAC proteins the rotation around the pore axis remains ambiguous. |