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- PDB-8ct9: CryoEM structure of human S-OPA1 assembled on lipid membrane in m... -

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Basic information

Entry
Database: PDB / ID: 8ct9
TitleCryoEM structure of human S-OPA1 assembled on lipid membrane in membrane-distal 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 / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion ...Regulation of Apoptosis / membrane tubulation / inner mitochondrial membrane organization / dynamin GTPase / cardiolipin binding / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / axon cytoplasm / visual perception / mitochondrion organization / neural tube closure / mitochondrial membrane / mitochondrial intermembrane space / cellular senescence / protein complex oligomerization / microtubule binding / microtubule / mitochondrial outer membrane / mitochondrial inner membrane / GTPase activity / apoptotic process / dendrite / GTP binding / negative regulation of apoptotic process / 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
CARDIOLIPIN / Dynamin-like 120 kDa protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsDu Pont, K.E. / Aydin, H.
Funding support United States, 1items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Dynamin-like 120 kDa protein, mitochondrial
F: Dynamin-like 120 kDa protein, mitochondrial
G: Dynamin-like 120 kDa protein, mitochondrial
H: Dynamin-like 120 kDa protein, mitochondrial
I: Dynamin-like 120 kDa protein, mitochondrial
J: Dynamin-like 120 kDa protein, mitochondrial
K: Dynamin-like 120 kDa protein, mitochondrial
L: Dynamin-like 120 kDa protein, mitochondrial
M: Dynamin-like 120 kDa protein, mitochondrial
N: Dynamin-like 120 kDa protein, mitochondrial
O: Dynamin-like 120 kDa protein, mitochondrial
P: Dynamin-like 120 kDa protein, mitochondrial
Q: Dynamin-like 120 kDa protein, mitochondrial
R: Dynamin-like 120 kDa protein, mitochondrial
S: Dynamin-like 120 kDa protein, mitochondrial
T: Dynamin-like 120 kDa protein, mitochondrial
U: Dynamin-like 120 kDa protein, mitochondrial
V: Dynamin-like 120 kDa protein, mitochondrial
W: Dynamin-like 120 kDa protein, mitochondrial
X: Dynamin-like 120 kDa protein, mitochondrial
Y: Dynamin-like 120 kDa protein, mitochondrial
Z: Dynamin-like 120 kDa protein, mitochondrial
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
e: Dynamin-like 120 kDa protein, mitochondrial
f: Dynamin-like 120 kDa protein, mitochondrial
g: Dynamin-like 120 kDa protein, mitochondrial
h: Dynamin-like 120 kDa protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,934,591125
Polymers3,801,36334
Non-polymers133,22891
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
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.: 34
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
#2: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 91 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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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: #1 / 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
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 FIELDBright-field microscopy / 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

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 128.619 ° / Axial rise/subunit: 8.04 Å / Axial symmetry: C1
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96152 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 676.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065201718
ELECTRON MICROSCOPYf_angle_d0.5742271660
ELECTRON MICROSCOPYf_chiral_restr0.284629762
ELECTRON MICROSCOPYf_plane_restr0.001834738
ELECTRON MICROSCOPYf_dihedral_angle_d9.7977893

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