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- PDB-7nie: putative glycerol kinase-like proteins anchored on an array of vo... -

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Basic information

Entry
Database: PDB / ID: 7nie
Titleputative glycerol kinase-like proteins anchored on an array of voltage dependent anion channels in the outer mitochondrial membrane of pig sperm mitochondria
Components
  • Glycerol kinase
  • Voltage-dependent anion-selective channel protein 2
KeywordsMEMBRANE PROTEIN / mitochondria / sperm
Function / homology
Function and homology information


PINK1-PRKN Mediated Mitophagy / Triglyceride biosynthesis / Ub-specific processing proteases / glycerol-3-phosphate biosynthetic process / voltage-gated monoatomic anion channel activity / mitochondrial outer membrane permeabilization / glycerol kinase / glycerol kinase activity / glycerol metabolic process / ceramide binding ...PINK1-PRKN Mediated Mitophagy / Triglyceride biosynthesis / Ub-specific processing proteases / glycerol-3-phosphate biosynthetic process / voltage-gated monoatomic anion channel activity / mitochondrial outer membrane permeabilization / glycerol kinase / glycerol kinase activity / glycerol metabolic process / ceramide binding / voltage-gated monoatomic ion channel activity / phosphatidylcholine binding / oxysterol binding / glycerol catabolic process / monoatomic anion transport / triglyceride metabolic process / cholesterol binding / lipid transport / porin activity / pore complex / sperm midpiece / mitochondrial outer membrane / nucleotide binding / mitochondrion / ATP binding / membrane
Similarity search - Function
Glycerol kinase, metazoa / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Eukaryotic porin/Tom40 ...Glycerol kinase, metazoa / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / FGGY family of carbohydrate kinases signature 1. / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Eukaryotic porin/Tom40 / Eukaryotic porin / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / Porin domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
glycerol kinase / Non-selective voltage-gated ion channel VDAC2
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å
AuthorsLeung, M.R. / Zeev-Ben-Mordehai, T.
Funding support Netherlands, 1items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Assembly

Deposited unit
A: Glycerol kinase
B: Glycerol kinase
C: Voltage-dependent anion-selective channel protein 2
D: Voltage-dependent anion-selective channel protein 2
E: Voltage-dependent anion-selective channel protein 2
F: Voltage-dependent anion-selective channel protein 2
G: Voltage-dependent anion-selective channel protein 2
H: Voltage-dependent anion-selective channel protein 2
I: Voltage-dependent anion-selective channel protein 2
J: Voltage-dependent anion-selective channel protein 2
K: Voltage-dependent anion-selective channel protein 2
L: Voltage-dependent anion-selective channel protein 2
M: Voltage-dependent anion-selective channel protein 2
N: Voltage-dependent anion-selective channel protein 2
O: Glycerol kinase
P: Glycerol kinase


Theoretical massNumber of molelcules
Total (without water)593,96816
Polymers593,96816
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Cross-linking mass spectrometry is consistent with the orientation assigned by rigid body fitting homology models into the subtomogram average map. All cross-links detected ...Evidence: cross-linking, Cross-linking mass spectrometry is consistent with the orientation assigned by rigid body fitting homology models into the subtomogram average map. All cross-links detected were between the [known] cytosolic face of VDAC and the [putative] membrane-facing surface of GK.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glycerol kinase


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
Voltage-dependent anion-selective channel protein 2


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: 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
Source (natural)Organism: Sus scrofa (pig) / Cellular location: midpiece / Organelle: mitochondria / Tissue: sperm
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1PEET1.13.0volume selection
2SerialEMimage acquisition
4IMOD4.10.25CTF correction
7UCSF Chimeramodel fitting
10PEET1.13.0final Euler assignment
12PEET1.13.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 536 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 3 / Num. of volumes extracted: 268 / Reference model: random particle from the dataset
Atomic model buildingProtocol: 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.

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