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Yorodumi- EMDB-4584: Structure and assembly of the mitochondrial membrane remodelling ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4584 | |||||||||
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Title | Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1 | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information dynamin GTPase / mitochondrial fusion / microtubule binding / microtubule / defense response to virus / GTPase activity / GTP binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (fungus) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.4 Å | |||||||||
Authors | Faelber K / Dietrich L / Noel J / Wollweber F / Pfitzner A / Muehleip A / Sanchez R / Kudryashev M / Chiaruttin N / Lilie H ...Faelber K / Dietrich L / Noel J / Wollweber F / Pfitzner A / Muehleip A / Sanchez R / Kudryashev M / Chiaruttin N / Lilie H / Schleger J / Rosenbaum E / Hessenberger M / Matthaeus C / Noe F / Roux A / van der Laan M / Kuehlbrandt W / Daumke O | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4584.map.gz | 30.8 MB | EMDB map data format | |
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Header (meta data) | emd-4584-v30.xml emd-4584.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4584_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_4584.png | 225.2 KB | ||
Masks | emd_4584_msk_1.map | 83.7 MB | Mask map | |
Others | emd_4584_half_map_1.map.gz emd_4584_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4584 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4584 | HTTPS FTP |
-Validation report
Summary document | emd_4584_validation.pdf.gz | 604.4 KB | Display | EMDB validaton report |
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Full document | emd_4584_full_validation.pdf.gz | 603.5 KB | Display | |
Data in XML | emd_4584_validation.xml.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4584 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4584 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4584.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4584_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered non-masked half-map #1
File | emd_4584_half_map_1.map | ||||||||||||
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Annotation | Unfiltered non-masked half-map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered non-masked half-map #2
File | emd_4584_half_map_2.map | ||||||||||||
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Annotation | Unfiltered non-masked half-map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mgm1
Entire | Name: Mgm1 |
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Components |
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-Supramolecule #1: Mgm1
Supramolecule | Name: Mgm1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: short isoform with C- and N-terminal truncations |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Mgm1
Macromolecule | Name: Mgm1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: dynamin GTPase |
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Source (natural) | Organism: Chaetomium thermophilum (fungus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: Chain A RD DNMMFITKKM IEIRNLLQKV GQGSTVTLPS IVVIGSQSSG KSSVLEAIVG HEFLPKGSNM ITRRPIELTL VNDPEAKVDY GEFPDLGLAR VTDFSLIQKT LTELNQSVTD DPIRLTIHSP NIPDLSLIDL PGYILKRKIT ELCDKYIRGP NIILAISAAD ...String: Chain A RD DNMMFITKKM IEIRNLLQKV GQGSTVTLPS IVVIGSQSSG KSSVLEAIVG HEFLPKGSNM ITRRPIELTL VNDPEAKVDY GEFPDLGLAR VTDFSLIQKT LTELNQSVTD DPIRLTIHSP NIPDLSLIDL PGYILKRKIT ELCDKYIRGP NIILAISAAD TDLANSTALQ ASRRVDPRGE RTIGVITKMD LVEPEKGAAI LSDRQYPLKL GYVGVISKGN LLASINRNEK NYFGSHPTEF GPDSGVSTGV MTLRKKLLQV LEQQMSSKLN ETTEAIQREL EETTYQFKVQ YNEQPMSAES YLAASLDDFK HQFHEFASSF GRPQLQTLLK DALDQKVLDQ LAARYWNRPI EDLSPAPREP DNIIDLPKAD PDSPYWHRQL DTACSGLTRL GVGRLAATVA ASAIQQHVEK LLDKSSFAKH PSARKVISDA AATVLADRSY ATSDGIEISL KPYKFDPDIQ PNEWAQGREH VVGVLQAELE QCQAAMKALE NSVGGRKKLK EVMSFVDKAR KGEIIVEGDH PSGAGGFSAA LLARGREAVF LRDRADILSL RIQAAKSRQC KTLTNKYYCP EVFLDAVATK LAQTAVLFLN VEMLNDFYVR FPREVEAKLH EHMHAGGGLE KFAREDPKVR RHLDLIRRKE LLETVLGKIE ELHRISSG C hain B DDN MMFITKKMIE IRNLLQKVGQ GSTVTLPSIV VIGSQSSGKS SVLEAIVGHE FLPKGSNMIT RRPIELTLVN DPEAKVDYGE FPDLGLARVT DFSLIQKTLT ELNQSVTDDP IRLTIHSPNI PDLSLIDLPG YILKRKITEL CDKYIRGPNI ILAISAADTD LANSTALQAS RRVDPRGERT IGVITKMDLV EPEKGAAILS DRQYPLKLGY VGVISKGNLL ASINRNEKNY FGSHPTEFGP DSGVSTGVMT LRKKLLQVLE QQMSSKLNET TEAIQRELEE TTYQFKVQYN EQPMSAESYL AASLDDFKHQ FHEFASSFGR PQLQTLLKDA LDQKVLDQLA ARYWNRPIED LSPAPREPDN IIDLPKADPD SPYWHRQLDT ACSGLTRLGV GRLAATVAAS AIQQHVEKLL DKSSFAKHPS ARKVISDAAA TVLADRSYAT SDGIEISLKP YKFDPDIQPN EWAQGREHVV GVLQAELEQC QAAMKALENS VGGRKKLKEV MSFVDKARKG EIIVEGDHPS GAGGFSAALL ARGREAVFLR DRADILSLRI QAAKSRQCKT LTNKYYCPEV FLDAVATKLA QTAVLFLNVE MLNDFYVRFP REVEAKLHEH MHAGGGLEKF AREDPKVRRH LDLIRRKELL ETVLGKIEEL HRISSGT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM HEPES, 200 mM NaCl, residual MgCl2, 9mM KCl. |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |