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- EMDB-26984: CryoEM structure of human S-OPA1 assembled on lipid membrane in m... -

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Basic information

Entry
Database: EMDB / ID: EMD-26984
TitleCryoEM structure of human S-OPA1 assembled on lipid membrane in membrane-distal state
Map dataRefine3D map
Sample
  • Complex: OPA1
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial
  • Ligand: CARDIOLIPIN
KeywordsGTPase / polymer / filament / membrane / remodeling / fusion / mitochondria / MEMBRANE PROTEIN
Function / homology
Function and homology information


Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / membrane bending activity / inner mitochondrial membrane organization / GTPase-dependent fusogenic activity / dynamin GTPase / cristae formation / peroxisome fission / : ...Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / membrane bending activity / inner mitochondrial membrane organization / GTPase-dependent fusogenic activity / dynamin GTPase / cristae formation / peroxisome fission / : / phosphatidic acid binding / cardiolipin binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / intracellular distribution of mitochondria / positive regulation of interleukin-17 production / protein complex oligomerization / positive regulation of T-helper 17 cell lineage commitment / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / visual perception / axon cytoplasm / Mitochondrial protein degradation / neural tube closure / mitochondrion organization / mitochondrial membrane / mitochondrial intermembrane space / endocytosis / cellular senescence / microtubule binding / microtubule / mitochondrial outer membrane / mitochondrial inner membrane / GTPase activity / apoptotic process / dendrite / negative regulation of apoptotic process / GTP binding / magnesium ion binding / mitochondrion / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Dynamin-like GTPase OPA1, C-terminal / Dynamin-like GTPase OPA1 C-terminal / 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
Dynamin-like GTPase OPA1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsDu Pont KE / Aydin H
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nature / Year: 2023
Title: Structural mechanism of mitochondrial membrane remodelling by human OPA1.
Authors: Alexander von der Malsburg / Gracie M Sapp / Kelly E Zuccaro / Alexander von Appen / Frank R Moss / Raghav Kalia / Jeremy A Bennett / Luciano A Abriata / Matteo Dal Peraro / Martin van der ...Authors: Alexander von der Malsburg / Gracie M Sapp / Kelly E Zuccaro / Alexander von Appen / Frank R Moss / Raghav Kalia / Jeremy A Bennett / Luciano A Abriata / Matteo Dal Peraro / Martin van der Laan / Adam Frost / Halil Aydin /
Abstract: Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate. The mechanochemical GTPase optic atrophy 1 (OPA1) ...Distinct morphologies of the mitochondrial network support divergent metabolic and regulatory processes that determine cell function and fate. The mechanochemical GTPase optic atrophy 1 (OPA1) influences the architecture of cristae and catalyses the fusion of the mitochondrial inner membrane. Despite its fundamental importance, the molecular mechanisms by which OPA1 modulates mitochondrial morphology are unclear. Here, using a combination of cellular and structural analyses, we illuminate the molecular mechanisms that are key to OPA1-dependent membrane remodelling and fusion. Human OPA1 embeds itself into cardiolipin-containing membranes through a lipid-binding paddle domain. A conserved loop within the paddle domain inserts deeply into the bilayer, further stabilizing the interactions with cardiolipin-enriched membranes. OPA1 dimerization through the paddle domain promotes the helical assembly of a flexible OPA1 lattice on the membrane, which drives mitochondrial fusion in cells. Moreover, the membrane-bending OPA1 oligomer undergoes conformational changes that pull the membrane-inserting loop out of the outer leaflet and contribute to the mechanics of membrane remodelling. Our findings provide a structural framework for understanding how human OPA1 shapes mitochondrial morphology and show us how human disease mutations compromise OPA1 functions.
History
DepositionMay 13, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26984.png

Downloads & links

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Map

FileDownload / File: emd_26984.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefine3D map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 420 pix.
= 699.72 Å		1.67 Å/pix.
x 420 pix.
= 699.72 Å		1.67 Å/pix.
x 420 pix.
= 699.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.666 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.014437045 - 0.019918822
Average (Standard dev.)0.000005556329 (±0.001219077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 699.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26984_msk_1.map
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Additional map: Postprocess map

Fileemd_26984_additional_1.map
AnnotationPostprocess map
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Half map: Refine3D half map 1

Fileemd_26984_half_map_1.map
AnnotationRefine3D half map 1
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Half map: Refine3D half map 2

Fileemd_26984_half_map_2.map
AnnotationRefine3D half map 2
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Sample components

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Entire : OPA1

EntireName: OPA1
Components
  • Complex: OPA1
    • Protein or peptide: Dynamin-like 120 kDa protein, mitochondrial
  • Ligand: CARDIOLIPIN

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Supramolecule #1: OPA1

SupramoleculeName: OPA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Uniprot ID: O60313 - HUMAN OPA1, Dynamin-like 120 kDa protein, mitochondrial
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 820 KDa

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Macromolecule #1: Dynamin-like 120 kDa protein, mitochondrial

MacromoleculeName: Dynamin-like 120 kDa protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 34 / Enantiomer: LEVO / EC number: dynamin GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.804789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MWRLRRAAVA CEVCQSLVKH SSGIKGSLPL QKLHLVSRSI YHSHHPTLKL QRPQLRTSFQ QFSSLTNLPL RKLKFSPIKY GYQPRRNFW PARLATRLLK LRYLILGSAV GGGYTAKKTF DQWKDMIPDL SEYKWIVPDI VWEIDEYIDF EKIRKALPSS E DLVKLAPD ...String:
MWRLRRAAVA CEVCQSLVKH SSGIKGSLPL QKLHLVSRSI YHSHHPTLKL QRPQLRTSFQ QFSSLTNLPL RKLKFSPIKY GYQPRRNFW PARLATRLLK LRYLILGSAV GGGYTAKKTF DQWKDMIPDL SEYKWIVPDI VWEIDEYIDF EKIRKALPSS E DLVKLAPD FDKIVESLSL LKDFFTSGSP EETAFRATDR GSESDKHFRK VSDKEKIDQL QEELLHTQLK YQRILERLEK EN KELRKLV LQKDDKGIHH RKLKKSLIDM YSEVLDVLSD YDASYNTQDH LPRVVVVGDQ SAGKTSVLEM IAQARIFPRG SGE MMTRSP VKVTLSEGPH HVALFKDSSR EFDLTKEEDL AALRHEIELR MRKNVKEGCT VSPETISLNV KGPGLQRMVL VDLP GVINT VTSGMAPDTK ETIFSISKAY MQNPNAIILC IQDGSVDAER SIVTDLVSQM DPHGRRTIFV LTKVDLAEKN VASPS RIQQ IIEGKLFPMK ALGYFAVVTG KGNSSESIEA IREYEEEFFQ NSKLLKTSML KAHQVTTRNL SLAVSDCFWK MVRESV EQQ ADSFKATRFN LETEWKNNYP RLRELDRNEL FEKAKNEILD EVISLSQVTP KHWEEILQQS LWERVSTHVI ENIYLPA AQ TMNSGTFNTT VDIKLKQWTD KQLPNKAVEV AWETLQEEFS RFMTEPKGKE HDDIFDKLKE AVKEESIKRH KWNDFAED S LRVIQHNALE DRSISDKQQW DAAIYFMEEA LQARLKDTEN AIENMVGPDW KKRWLYWKNR TQEQCVHNET KNELEKMLK CNEEHPAYLA SDEITTVRKN LESRGVEVDP SLIKDTWHQV YRRHFLKTAL NHCNLCRRGF YYYQRHFVDS ELECNDVVLF WRIQRMLAI TANTLRQQLT NTEVRRLEKN VKEVLEDFAE DGEKKIKLLT GKRVQLAEDL KKVREIQEKL DAFIEALHQE K

UniProtKB: Dynamin-like GTPase OPA1, mitochondrial

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Macromolecule #2: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 2 / Number of copies: 91 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.04 Å
Applied symmetry - Helical parameters - Δ&Phi: 128.619 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 96152
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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