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- EMDB-5644: Two-dimensional crystals of sMgm1 over a monolayer with a lipid c... -

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Basic information

Entry
Database: EMDB / ID: EMD-5644
TitleTwo-dimensional crystals of sMgm1 over a monolayer with a lipid composition identical to that of the mitochondrial inner membrane
Map dataThree dimensional reconstruction from tilted images of a two-dimensional crystal of sMgm1 in the absence of substrate
Sample
  • Sample: Small isoform of yeast Mgm1
  • Protein or peptide: Mitochondrial genome maintenance 1
KeywordsMitochondrial proteins / mitochondrial membrane fusion / mitochondrial cristae maintenance / yeast / DRP / sMgm1
Function / homology
Function and homology information


mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / Regulation of Apoptosis / membrane bending / mitochondrion inheritance / mitochondrial inner membrane fusion / membrane tubulation / GTPase-dependent fusogenic activity / membrane bending activity / heme transport ...mitochondrial inner boundary membrane / mitochondrial outer membrane fusion / Regulation of Apoptosis / membrane bending / mitochondrion inheritance / mitochondrial inner membrane fusion / membrane tubulation / GTPase-dependent fusogenic activity / membrane bending activity / heme transport / dynamin GTPase / cristae formation / 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 / mitochondrial outer membrane / microtubule / mitochondrial inner membrane / GTPase activity / GTP binding / mitochondrion / membrane / metal ion binding / cytoplasm
Similarity search - Function
Dynamin, GTPase region, conserved site / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / GTPase effector domain / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin ...Dynamin, GTPase region, conserved site / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / GTPase effector domain / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron crystallography / negative staining / Resolution: 24.0 Å
AuthorsDevay RM / Dominguez-Ramirez L / Lackner LL / Hoppins S / Stahlberg H / Nunnari J
CitationJournal: J Cell Biol / Year: 2009
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
DepositionApr 28, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 3, 2013-
UpdateJul 3, 2013-
Current statusJul 3, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5644_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5644.map.gz / Format: CCP4 / Size: 120.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree dimensional reconstruction from tilted images of a two-dimensional crystal of sMgm1 in the absence of substrate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.66 Å/pix.
x 201 pix.
= 932. Å		4.66 Å/pix.
x 401 pix.
= 932. Å		4.66 Å/pix.
x 401 pix.
= 932. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel size
XYZ
EMDB info.4.664.664.66
CCP4 map header4.664.664.66
EM Navigator Movie #1111
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-250.0 - 199.840820309999998
Average (Standard dev.)0.00980678 (±47.39643478)
SymmetrySpace group: 143
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-100
Dimensions401401201
Spacing200200200
CellA=B=C: 932.0 Å
α: 90.0 ° / β: 90.0 ° / γ: 120.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.664.664.66
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z932.000932.000932.000
α/β/γ90.00090.000120.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-200-200-100
NC/NR/NS401401201
D min/max/mean-250.000199.8410.010

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Supplemental data

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Sample components

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Entire : Small isoform of yeast Mgm1

EntireName: Small isoform of yeast Mgm1
Components
  • Sample: Small isoform of yeast Mgm1
  • Protein or peptide: Mitochondrial genome maintenance 1

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Supramolecule #1000: Small isoform of yeast Mgm1

SupramoleculeName: 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
Molecular weightExperimental: 76 MDa / Theoretical: 76 MDa / Method: Sedimentation

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Macromolecule #1: Mitochondrial genome maintenance 1

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: mitochondrion / Location in cell: inner mitochondrial membrane
Molecular weightExperimental: 76 MDa / Theoretical: 76 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Dynamin-like GTPase MGM1, mitochondrial / GO: mitochondrial fusion
InterPro: Dynamin, Dynamin, GTPase domain, Dynamin, GTPase region, conserved site, GTPase effector domain

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl
StainingType: NEGATIVE
Details: Grids were floated on 2% uranyl acetate for 10 seconds twice.
GridDetails: 200 mesh copper grid with thin carbon support, non-glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER
DetailsCrystals were grown on a lipid monolayer.
Crystal formationDetails: Crystals were grown on a lipid monolayer.

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Electron microscopy

MicroscopeJEOL 1230
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateJul 2, 2009
Image recordingNumber real images: 35
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination 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 stageSpecimen 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

DetailsImages were processed entirely using 2dx.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.0 Å / Software - Name: 2DX
Crystal parametersUnit cell - A: 200 Å / Unit cell - B: 200 Å / Unit cell - γ: 120 ° / Plane group: P 3

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