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- PDB-8vm4: CryoEM structure of human S-OPA1 assembled on lipid membrane cont... -

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Basic information

Entry
Database: PDB / ID: 8vm4
TitleCryoEM structure of human S-OPA1 assembled on lipid membrane containing brominated cardiolipin in membrane-adjacent state
ComponentsDynamin-like 120 kDa protein, mitochondrial
KeywordsMEMBRANE PROTEIN / GTPase / polymer / filament / membrane / remodeling / fusion / mitochondria
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 / mitochondrion organization / neural tube closure / 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 / cytosol / cytoplasm
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsZuccaro, K.E. / Aydin, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM150942 United States
American Heart Association23POST1020756 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1.
Authors: Sirikrishna Thatavarthy / Luciano A Abriata / Fernando Teixeira Pinto Meireles / Kelly E Zuccaro / Akhil Gargey Iragavarapu / Gabriela May Sullivan / Frank R Moss / Adam Frost / Matteo Dal ...Authors: Sirikrishna Thatavarthy / Luciano A Abriata / Fernando Teixeira Pinto Meireles / Kelly E Zuccaro / Akhil Gargey Iragavarapu / Gabriela May Sullivan / Frank R Moss / Adam Frost / Matteo Dal Peraro / Halil Aydin /
Abstract: Cardiolipin is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the ...Cardiolipin is a mitochondria-specific phospholipid that forms heterotypic interactions with membrane-shaping proteins and regulates the dynamic remodeling and function of mitochondria. However, the precise mechanisms through which cardiolipin influences mitochondrial morphology are not well understood. In this study, employing molecular dynamics simulations, we determined that cardiolipin molecules extensively engage with the paddle domain of mitochondrial fusion protein OPA1, which controls membrane-shaping mechanisms. Structure-function analysis confirmed the interactions between cardiolipin and two conserved motifs of OPA1 at the membrane-binding sites. We further developed a bromine-labeled cardiolipin probe to enhance cryoEM contrast and characterized the structure of OPA1 assemblies bound to the cardiolipin brominated lipid bilayers. Our images provide direct evidence of cardiolipin enrichment within the OPA1-binding leaflet. Last, we observed a decrease in membrane remodeling activity for OPA1 in lipid compositions with increasing concentrations of monolyso-cardiolipin. This suggests that the partial replacement of cardiolipin by monolyso-cardiolipin, as observed in Barth syndrome, alters the malleability of the membrane and compromises proper remodeling. Together, these data provide insights into how biological membranes regulate the mechanisms governing mitochondrial homeostasis.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-like 120 kDa protein, mitochondrial
B: Dynamin-like 120 kDa protein, mitochondrial
C: Dynamin-like 120 kDa protein, mitochondrial
D: Dynamin-like 120 kDa protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)447,2194
Polymers447,2194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Dynamin-like 120 kDa protein, mitochondrial / Optic atrophy protein 1


Mass: 111804.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPA1, KIAA0567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60313, dynamin GTPase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: OPA1 / Type: COMPLEX
Details: Uniprot ID: O60313 - HUMAN OPA1, Dynamin-like 120 kDa protein, mitochondrial
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.82 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 82 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 128.642 ° / Axial rise/subunit: 7.69 Å / Axial symmetry: C1
3D reconstructionResolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11469 / Symmetry type: HELICAL

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