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- EMDB-10064: Structure of s-Mgm1 decorating the inner surface of tubulated lip... -

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Basic information

Entry
Database: EMDB / ID: EMD-10064
TitleStructure of s-Mgm1 decorating the inner surface of tubulated lipid membranes
Map data
SampleMgm1:
Putative mitochondrial dynamin protein
Function / homology
Function and homology information


GTPase activity / GTP binding
Dynamin central domain / Dynamin, GTPase domain / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin family / Dynamin central region / Dynamin-type guanine nucleotide-binding (G) domain signature. ...Dynamin central domain / Dynamin, GTPase domain / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin family / Dynamin central region / Dynamin-type guanine nucleotide-binding (G) domain signature. / GED domain profile. / Dynamin-type guanine nucleotide-binding (G) domain profile.
Putative mitochondrial dynamin protein
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 20.6 Å
AuthorsFaelber K / Dietrich L / Noel JK / Sanchez R / Kudryashev M / Kuelbrandt W / Daumke O
Funding support Germany, 1 items
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 / 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.
Validation ReportPDB-ID: 6rzv

SummaryFull reportAbout validation report
History
DepositionJun 13, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 24, 2019-
UpdateJul 31, 2019-
Current statusJul 31, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.5
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  • Surface view with fitted model
  • Atomic models: : PDB-6rzv
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6rzv
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10064.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 160 pix.
= 432. Å
2.7 Å/pix.
x 160 pix.
= 432. Å
2.7 Å/pix.
x 160 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.0248219 - 3.5259705
Average (Standard dev.)0.071875826 (±0.32441175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.0253.5260.072

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Supplemental data

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Mask #1

Fileemd_10064_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Mgm1

EntireName: Mgm1 / Details: short isoform with C- and N-terminal truncations / Number of components: 2

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Component #1: protein, Mgm1

ProteinName: Mgm1 / Details: short isoform with C- and N-terminal truncations / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Putative mitochondrial dynamin protein

ProteinName: Putative mitochondrial dynamin protein / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 77.360172 kDa
SourceSpecies: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/mL
Buffer solution: 20 mM HEPES, 200 mM NaCl, residual MgCl2, 9mM KCl.
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 70 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 53000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 1792 / Number of class averages: 1
3D reconstructionAlgorithm: BACK PROJECTION / Software: Dynamo
CTF correction: CTF determination was done by Gctf and correction was performed by ctfphaseflip from Imod
Resolution: 20.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Half sets were generated not even-odd but as upper and lower-halves of particles in given tomogram
Euler angles: subtomogram averaging by cross correlation maximization
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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