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- PDB-8efr: CryoEM of the soluble OPA1 interfaces with GDP-AlFx bound from th... -

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Basic information

Entry
Database: PDB / ID: 8efr
TitleCryoEM of the soluble OPA1 interfaces with GDP-AlFx bound from the helical assembly on a lipid membrane
ComponentsDynamin-like 120 kDa protein, form S1
KeywordsLIPID BINDING PROTEIN / GTPase / Dynamin-family protein / mitochondrial fusion protein / mitochondria / Optic Atrophy
Function / homology
Function and homology information


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 / cardiolipin binding / mitochondrial fission / mitochondrial fusion / GTP metabolic process / negative regulation of release of cytochrome c from mitochondria / axonal transport of mitochondrion / mitochondrial crista / positive regulation of interleukin-17 production / protein complex oligomerization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of T-helper 17 cell lineage commitment / axon cytoplasm / Mitochondrial protein degradation / visual perception / neural tube closure / mitochondrion organization / mitochondrial membrane / mitochondrial intermembrane space / cellular senescence / 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 / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / : / Dynamin-like GTPase OPA1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.48 Å
AuthorsNyenhuis, S.B. / Wu, X. / Stanton, A.E. / Strub, M.P. / Yim, Y.I. / Canagarajah, B. / Hinshaw, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2023
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.
History
DepositionSep 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-like 120 kDa protein, form S1
B: Dynamin-like 120 kDa protein, form S1
C: Dynamin-like 120 kDa protein, form S1
K: Dynamin-like 120 kDa protein, form S1
D: Dynamin-like 120 kDa protein, form S1
L: Dynamin-like 120 kDa protein, form S1
E: Dynamin-like 120 kDa protein, form S1
M: Dynamin-like 120 kDa protein, form S1
F: Dynamin-like 120 kDa protein, form S1
N: Dynamin-like 120 kDa protein, form S1
G: Dynamin-like 120 kDa protein, form S1
O: Dynamin-like 120 kDa protein, form S1
H: Dynamin-like 120 kDa protein, form S1
P: Dynamin-like 120 kDa protein, form S1
I: Dynamin-like 120 kDa protein, form S1
Q: Dynamin-like 120 kDa protein, form S1
J: Dynamin-like 120 kDa protein, form S1
R: Dynamin-like 120 kDa protein, form S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,617,69890
Polymers1,606,72518
Non-polymers10,97272
Water00
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, form S1


Mass: 89262.516 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPA1, KIAA0567 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O60313
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: cryoEM of the soluble OPA1 interfaces with GDP-AlFx bound from the helical assembly on a lipid membrane
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: RIL
Buffer solutionpH: 7.2
SpecimenEmbedding 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 FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 37.439 ° / Axial rise/subunit: 12.933 Å / Axial symmetry: C1
3D reconstructionResolution: 5.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 598503 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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