[English] 日本語
Yorodumi
- EMDB-10065: Structure of s-Mgm1 decorating the inner surface of tubulated lip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10065
TitleStructure of s-Mgm1 decorating the inner surface of tubulated lipid membranes in the GTPgammaS bound state
Map data
Sample
  • Complex: Mgm1
    • Protein or peptide: Putative mitochondrial dynamin protein
Function / homology
Function and homology information


organelle organization / GTPase activity / GTP 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
Putative mitochondrial dynamin protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 18.8 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 / ...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, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 24, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.67
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.67
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rzw
  • Surface level: 0.67
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rzw
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10065.png

Downloads & links

-
Map

FileDownload / File: emd_10065.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.67 / Movie #1: 0.67
Minimum - Maximum-1.8122222 - 4.289866
Average (Standard dev.)0.1272207 (±0.49611065)
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-1.8124.2900.127

-
Supplemental data

-
Mask #1

Fileemd_10065_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered non-masked half-map #1

Fileemd_10065_half_map_1.map
AnnotationUnfiltered non-masked half-map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered non-masked half-map #2

Fileemd_10065_half_map_2.map
AnnotationUnfiltered non-masked half-map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mgm1

EntireName: Mgm1
Components
  • Complex: Mgm1
    • Protein or peptide: Putative mitochondrial dynamin protein

-
Supramolecule #1: Mgm1

SupramoleculeName: Mgm1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: short isoform with N- and C-terminal truncations
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Putative mitochondrial dynamin protein

MacromoleculeName: Putative mitochondrial dynamin protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 77.360172 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EEIMRDDNMM FITKKMIEIR NLLQKVGQGS TVTLPSIVVI GSQSSGKSSV LEAIVGHEFL PKGSNMITRR PIELTLVNDP EAKVDYGEF PDLGLARVTD FSLIQKTLTE LNQSVPESEC VTDDPIRLTI HSPNIPDLSL IDLPGYIQVA GENQPRELKR K ITELCDKY ...String:
EEIMRDDNMM FITKKMIEIR NLLQKVGQGS TVTLPSIVVI GSQSSGKSSV LEAIVGHEFL PKGSNMITRR PIELTLVNDP EAKVDYGEF PDLGLARVTD FSLIQKTLTE LNQSVPESEC VTDDPIRLTI HSPNIPDLSL IDLPGYIQVA GENQPRELKR K ITELCDKY IRGPNIILAI SAADTDLANS TALQASRRVD PRGERTIGVI TKMDLVEPEK GAAILSDRQY PLKLGYVGVI SK LPPQSGL FRRDTGNLLA SINRNEKNYF GSHPTEFGPD SGVSTGVMTL RKKLLQVLEQ QMSSKLNETT EAIQRELEET TYQ FKVQYN EQPMSAESYL AASLDDFKHQ FHEFASSFGR PQLQTLLKDA LDQKVLDQLA ARYWNRPIED LSPAPREPDN IIDL PKADP DSPYWHRQLD TACSGLTRLG VGRLAATVAA SAIQQHVEKL LDKSSFAKHP SARKVISDAA ATVLADRSYA TSDGI EISL KPYKFDPDIQ PNEWAQGREH VVGVLQAELE QCQAAMKALE NSVGGRKKLK EVMSFVDKAR KGEIIVEGDH PSGAGG FSA ALLARGREAV FLRDRADILS LRIQAAKSRQ CKTLTNKYYC PEVFLDAVAT KLAQTAVLFL NVEMLNDFYV RFPREVE AK LHEHMHAGGG LEKFAREDPK VRRHLDLIRR KELLETVLGK IEELHRISSG TAG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 200 mM NaCl, residual MgCl2, 9mM KCl.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 2 / Number images used: 4751
Reference model: global average of the particles rotated to the known initial orientations
Method: Geometry-assisted particle picking form tube surfaces
Software - Name: Dynamo (ver. 1.1.266) / Details: with the use of Dynamo Catalogue system
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.06)detection
IMOD (ver. 4.10)correction

Details: CTF determination was done by Gctf and correction was performed by ctfphaseflip from IMOD
Final 3D classificationNumber classes: 1 / Avg.num./class: 1820 / Software - Name: Dynamo (ver. 1.1.266)
Final angle assignmentType: OTHER / Software - Name: Dynamo (ver. 1.1.266) / Software - details: independent half-set refinement
Details: subtomogram averaging by cross correlation maximization
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 18.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.1.266)
Details: Half sets were generated not even-odd but as upper and lower-halves of particles in given tomogram
Number subtomograms used: 1820
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more