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- PDB-6rzt: Structure of s-Mgm1 decorating the outer surface of tubulated lip... -

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Basic information

Entry
Database: PDB / ID: 6rzt
TitleStructure of s-Mgm1 decorating the outer surface of tubulated lipid membranes
ComponentsPutative mitochondrial dynamin protein
KeywordsCONTRACTILE PROTEIN / mitochondrial protein / membrane remodelling / GTPase / mitochondrial dynamics / subtomogram averaging
Function / homology
Function and homology information


GTPase-dependent fusogenic activity / membrane bending activity / dynamin GTPase / mitochondrial intermembrane space / mitochondrial inner membrane / GTPase activity / lipid binding / GTP binding / metal ion binding
Similarity search - Function
Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain ...Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynamin-like GTPase MGM1, mitochondrial
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 14.7 Å
AuthorsFaelber, K. / Dietrich, L. / Noel, J.K. / Sanchez, R. / Kudryashev, M. / Kuehlbrandt, W. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2019
Title: Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1.
Authors: Katja Faelber / Lea Dietrich / Jeffrey K Noel / Florian Wollweber / Anna-Katharina Pfitzner / Alexander Mühleip / Ricardo Sánchez / Misha Kudryashev / Nicolas Chiaruttini / Hauke Lilie / ...Authors: Katja Faelber / Lea Dietrich / Jeffrey K Noel / Florian Wollweber / Anna-Katharina Pfitzner / Alexander Mühleip / Ricardo Sánchez / Misha Kudryashev / Nicolas Chiaruttini / Hauke Lilie / Jeanette Schlegel / Eva Rosenbaum / Manuel Hessenberger / Claudia Matthaeus / Séverine Kunz / Alexander von der Malsburg / Frank Noé / Aurélien Roux / Martin van der Laan / Werner Kühlbrandt / Oliver Daumke /
Abstract: Balanced fusion and fission are key for the proper function and physiology of mitochondria. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial ...Balanced fusion and fission are key for the proper function and physiology of mitochondria. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals. Mgm1 is required for the preservation of mitochondrial DNA in yeast, whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy-a genetic disorder that affects the optic nerve. Mgm1 and OPA1 are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space. Yeast strains that express temperature-sensitive mutants of Mgm1 or mammalian cells that lack OPA1 display fragmented mitochondria, which suggests that Mgm1 and OPA1 have an important role in inner-membrane fusion. Consistently, only the mitochondrial outer membrane-not the inner membrane-fuses in the absence of functional Mgm1. Mgm1 and OPA1 have also been shown to maintain proper cristae architecture; for example, OPA1 prevents the release of pro-apoptotic factors by tightening crista junctions. Finally, the short form of OPA1 localizes to mitochondrial constriction sites, where it presumably promotes mitochondrial fission. How Mgm1 and OPA1 perform their diverse functions in membrane fusion, scission and cristae organization is at present unknown. Here we present crystal and electron cryo-tomography structures of Mgm1 from Chaetomium thermophilum. Mgm1 consists of a GTPase (G) domain, a bundle signalling element domain, a stalk, and a paddle domain that contains a membrane-binding site. Biochemical and cell-based experiments demonstrate that the Mgm1 stalk mediates the assembly of bent tetramers into helical filaments. Electron cryo-tomography studies of Mgm1-decorated lipid tubes and fluorescence microscopy experiments on reconstituted membrane tubes indicate how the tetramers assemble on positively or negatively curved membranes. Our findings convey how Mgm1 and OPA1 filaments dynamically remodel the mitochondrial inner membrane.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 18, 2020Group: Data collection / Category: em_imaging_optics
Item: _em_imaging_optics.chr_aberration_corrector / _em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
A: Putative mitochondrial dynamin protein
B: Putative mitochondrial dynamin protein
C: Putative mitochondrial dynamin protein
D: Putative mitochondrial dynamin protein
E: Putative mitochondrial dynamin protein
F: Putative mitochondrial dynamin protein
G: Putative mitochondrial dynamin protein
H: Putative mitochondrial dynamin protein
I: Putative mitochondrial dynamin protein
J: Putative mitochondrial dynamin protein
K: Putative mitochondrial dynamin protein
L: Putative mitochondrial dynamin protein


Theoretical massNumber of molelcules
Total (without water)928,32212
Polymers928,32212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19980 Å2
ΔGint-56 kcal/mol
Surface area397400 Å2
MethodPISA

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Components

#1: Protein
Putative mitochondrial dynamin protein


Mass: 77360.172 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0065850 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGC7
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Mgm1 / Type: COMPLEX / Details: short isoform with C- and N-terminal truncations / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 20 mM HEPES, 200 mM NaCl, residual MgCl2, 9mM KCl.
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was prepared in the described buffer. Just before freezing 6 nm colloidal gold fiducial marker were added to the sample in a 1:1 ratio.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 53000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2 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
IDNameVersionCategoryDetails
1Dynamo1.1.226volume selection
2SerialEM3.6image acquisitionDose symmetric tilt scheme (Hagen et al, JSB, 2017)
4Gctf1.06CTF correctiondetection
5IMOD4.1CTF correctioncorrection
12Dynamo1.1.266final Euler assignmentindependent half-set refinement
13Dynamo1.3classification
14Dynamo1.1.2263D reconstruction
CTF correctionDetails: CTF determination was done by Gctf and correction was performed by ctfphaseflip from IMOD
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 14.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11474
Details: Half sets were generated not even-odd but as upper and lower-halves of particles in given tomogram
Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Geometry-assisted particle picking form tube surfaces
Details: with the use of Dynamo Catalogue system / Num. of tomograms: 15 / Num. of volumes extracted: 12440
Reference model: global average of the particles rotated to the known initial orientations

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