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- EMDB-5644: Two-dimensional crystals of sMgm1 over a monolayer with a lipid c... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5644 | |||||||||
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Title | Two-dimensional crystals of sMgm1 over a monolayer with a lipid composition identical to that of the mitochondrial inner membrane | |||||||||
![]() | Three dimensional reconstruction from tilted images of a two-dimensional crystal of sMgm1 in the absence of substrate | |||||||||
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![]() | Mitochondrial proteins / mitochondrial membrane fusion / mitochondrial cristae maintenance / yeast / DRP / sMgm1 | |||||||||
Function / homology | ![]() mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / Regulation of Apoptosis / mitochondrion inheritance / mitochondrial inner membrane fusion / heme transport / mitochondrial genome maintenance / phosphatidic acid binding / cardiolipin binding / mitochondrial membrane organization ...mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / Regulation of Apoptosis / mitochondrion inheritance / mitochondrial inner membrane fusion / heme transport / mitochondrial genome maintenance / phosphatidic acid binding / cardiolipin binding / mitochondrial membrane organization / phosphatidylinositol-3,5-bisphosphate binding / mitochondrial fusion / phosphatidylserine binding / mitochondrial crista / mitochondrion organization / mitochondrial intermembrane space / microtubule binding / microtubule / membrane fusion / mitochondrial inner membrane / GTPase activity / GTP binding / mitochondrion / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron crystallography / negative staining / Resolution: 24.0 Å | |||||||||
![]() | Devay RM / Dominguez-Ramirez L / Lackner LL / Hoppins S / Stahlberg H / Nunnari J | |||||||||
![]() | ![]() Title: Coassembly of Mgm1 isoforms requires cardiolipin and mediates mitochondrial inner membrane fusion. Authors: Rachel M DeVay / Lenin Dominguez-Ramirez / Laura L Lackner / Suzanne Hoppins / Henning Stahlberg / Jodi Nunnari / ![]() Abstract: Two dynamin-related protein (DRP) families are essential for fusion of the outer and inner mitochondrial membranes, Fzo1 (yeast)/Mfn1/Mfn2 (mammals) and Mgm1 (yeast)/Opa1 (mammals), respectively. ...Two dynamin-related protein (DRP) families are essential for fusion of the outer and inner mitochondrial membranes, Fzo1 (yeast)/Mfn1/Mfn2 (mammals) and Mgm1 (yeast)/Opa1 (mammals), respectively. Fzo1/Mfns possess two medial transmembrane domains, which place their critical GTPase and coiled-coil domains in the cytosol. In contrast, Mgm1/Opa1 are present in cells as long (l) isoforms that are anchored via the N terminus to the inner membrane, and short (s) isoforms were predicted to be soluble in the intermembrane space. We addressed the roles of Mgm1 isoforms and how DRPs function in membrane fusion. Our analysis indicates that in the absence of a membrane, l- and s-Mgm1 both exist as inactive GTPase monomers, but that together in trans they form a functional dimer in a cardiolipin-dependent manner that is the building block for higher-order assemblies. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 64.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Three dimensional reconstruction from tilted images of a two-dimensional crystal of sMgm1 in the absence of substrate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 143 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Small isoform of yeast Mgm1
Entire | Name: Small isoform of yeast Mgm1 |
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Components |
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-Supramolecule #1000: Small isoform of yeast Mgm1
Supramolecule | Name: Small isoform of yeast Mgm1 / type: sample / ID: 1000 Details: The sample aggregates as the oligomer observed by electron microscopy only in the presence of lipids, particularly those making up the inner mitochondrial membrane. Oligomeric state: trimer of dimers / Number unique components: 1 |
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Molecular weight | Experimental: 76 MDa / Theoretical: 76 MDa / Method: Sedimentation |
-Macromolecule #1: Mitochondrial genome maintenance 1
Macromolecule | Name: Mitochondrial genome maintenance 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Dynamin-like GTPase MGM1, mitochondrial Details: Lipid monolayer with same composition as inner mitochondrial membranes Number of copies: 6 / Oligomeric state: Trimer of dimers / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 76 MDa / Theoretical: 76 MDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Dynamin-like GTPase MGM1, mitochondrial / GO: mitochondrial fusion InterPro: Dynamin, Dynamin, GTPase domain, Dynamin, GTPase region, conserved site, GTPase effector domain |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | electron crystallography |
Aggregation state | 2D array |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 20 mM Tris-HCl |
Staining | Type: NEGATIVE Details: Grids were floated on 2% uranyl acetate for 10 seconds twice. |
Grid | Details: 200 mesh copper grid with thin carbon support, non-glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
Details | Crystals were grown on a lipid monolayer. |
Crystal formation | Details: Crystals were grown on a lipid monolayer. |
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Electron microscopy
Microscope | JEOL 1230 |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | Jul 2, 2009 |
Image recording | Number real images: 35 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: JEOL / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 ° |
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Image processing
Details | Images were processed entirely using 2dx. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Software - Name: 2DX |
Crystal parameters | Unit cell - A: 200 Å / Unit cell - B: 200 Å / Unit cell - γ: 120 ° / Plane group: P 3 |