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- PDB-8eff: CryoEM of the soluble OPA1 tetramer from the GDP-AlFx bound helic... -
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Basic information
Entry | Database: PDB / ID: 8eff | ||||||
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Title | CryoEM of the soluble OPA1 tetramer from the GDP-AlFx bound helical assembly on a lipid membrane | ||||||
![]() | Dynamin-like 120 kDa protein, form S1 | ||||||
![]() | LIPID BINDING PROTEIN / GTPase / Dynamin-family protein / mitochondrial fusion protein / mitochondria / Optic Atrophy | ||||||
Function / homology | ![]() Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / GTPase-dependent fusogenic activity / membrane bending activity / inner mitochondrial membrane organization / dynamin GTPase / cristae formation / mitochondrial genome maintenance / phosphatidic acid binding ...Regulation of Apoptosis / mitochondrial inner membrane fusion / membrane tubulation / GTPase-dependent fusogenic activity / membrane bending activity / inner mitochondrial membrane organization / dynamin GTPase / cristae formation / mitochondrial genome maintenance / phosphatidic acid binding / mitochondrial fission / cardiolipin binding / positive regulation of T-helper 17 cell lineage commitment / GTP metabolic process / mitochondrial fusion / axonal transport of mitochondrion / negative regulation of release of cytochrome c from mitochondria / mitochondrial crista / positive regulation of interleukin-17 production / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / axon cytoplasm / visual perception / mitochondrion organization / Mitochondrial protein degradation / neural tube closure / mitochondrial membrane / cellular senescence / mitochondrial intermembrane space / protein complex oligomerization / microtubule binding / mitochondrial outer membrane / microtubule / mitochondrial inner membrane / GTPase activity / dendrite / negative regulation of apoptotic process / GTP binding / apoptotic process / magnesium ion binding / mitochondrion / nucleoplasm / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.48 Å | ||||||
![]() | Nyenhuis, S.B. / Wu, X. / Stanton, A.E. / Strub, M.P. / Yim, Y.I. / Canagarajah, B. / Hinshaw, J.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: OPA1 helical structures give perspective to mitochondrial dysfunction. Authors: Sarah B Nyenhuis / Xufeng Wu / Marie-Paule Strub / Yang-In Yim / Abigail E Stanton / Valentina Baena / Zulfeqhar A Syed / Bertram Canagarajah / John A Hammer / Jenny E Hinshaw / ![]() Abstract: Dominant optic atrophy is one of the leading causes of childhood blindness. Around 60-80% of cases are caused by mutations of the gene that encodes optic atrophy protein 1 (OPA1), a protein that has ...Dominant optic atrophy is one of the leading causes of childhood blindness. Around 60-80% of cases are caused by mutations of the gene that encodes optic atrophy protein 1 (OPA1), a protein that has a key role in inner mitochondrial membrane fusion and remodelling of cristae and is crucial for the dynamic organization and regulation of mitochondria. Mutations in OPA1 result in the dysregulation of the GTPase-mediated fusion process of the mitochondrial inner and outer membranes. Here we used cryo-electron microscopy methods to solve helical structures of OPA1 assembled on lipid membrane tubes, in the presence and absence of nucleotide. These helical assemblies organize into densely packed protein rungs with minimal inter-rung connectivity, and exhibit nucleotide-dependent dimerization of the GTPase domains-a hallmark of the dynamin superfamily of proteins. OPA1 also contains several unique secondary structures in the paddle domain that strengthen its membrane association, including membrane-inserting helices. The structural features identified in this study shed light on the effects of pathogenic point mutations on protein folding, inter-protein assembly and membrane interactions. Furthermore, mutations that disrupt the assembly interfaces and membrane binding of OPA1 cause mitochondrial fragmentation in cell-based assays, providing evidence of the biological relevance of these interactions. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 883.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28063MC ![]() 8eewC ![]() 8ef7C ![]() 8efrC ![]() 8efsC ![]() 8eftC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 89262.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-ALF / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-K / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: cryoEM of the soluble OPA1 tetramer from the GDP-AlFx bound helical assembly on a lipid membrane Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Helical symmerty | Angular rotation/subunit: 37.439 ° / Axial rise/subunit: 12.933 Å / Axial symmetry: C1 | |||||||||
3D reconstruction | Resolution: 5.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 598503 / Symmetry type: HELICAL | |||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||
Atomic model building | PDB-ID: 6JTG |