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- PDB-8v8t: Asymmetrical subunit from a Drp1 lattice on PA nanotubes -

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Basic information

Entry
Database: PDB / ID: 8v8t
TitleAsymmetrical subunit from a Drp1 lattice on PA nanotubes
ComponentsDynamin-1-like protein
KeywordsHYDROLASE / membrane remodeling GTPase
Function / homology
Function and homology information


mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / peroxisome fission / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / peroxisome fission / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / heart contraction / intracellular distribution of mitochondria / protein complex oligomerization / brush border / clathrin-coated pit / GTPase activator activity / positive regulation of protein secretion / mitochondrion organization / small GTPase binding / synaptic vesicle membrane / endocytosis / calcium ion transport / rhythmic process / peroxisome / regulation of gene expression / microtubule binding / microtubule / mitochondrial outer membrane / GTPase activity / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / 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-1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.73 Å
AuthorsRochon, K. / Peng, R. / Hutson, A.N. / Stagg, S.M. / Mears, J.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM125844 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM108753 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM143805 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM139324 United States
CitationJournal: J Mol Biol / Year: 2025
Title: The Structure of the Drp1 Lattice on Membrane.
Authors: Ruizhi Peng / Kristy Rochon / Anelise N Hutson / Scott M Stagg / Jason A Mears /
Abstract: Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a ...Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanisms. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. We identified two states of the Drp1 lattice among the heterogenous dataset representing conformational changes around hinge 1. Additionally, we observed contact between Drp1 and membrane that can be assigned to the variable domain sequence. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynamin-1-like protein
B: Dynamin-1-like protein
C: Dynamin-1-like protein
D: Dynamin-1-like protein


Theoretical massNumber of molelcules
Total (without water)330,4354
Polymers330,4354
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Dynamin-1-like protein / Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less ...Dnm1p/Vps1p-like protein / DVLP / Dynamin family member proline-rich carboxyl-terminal domain less / Dymple / Dynamin-like protein / Dynamin-like protein 4 / Dynamin-like protein IV / HdynIV / Dynamin-related protein 1


Mass: 82608.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, DLP1, DRP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O00429, dynamin GTPase
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Tetramer complex of Drp1 from a lattice / Type: COMPLEX
Details: Asymmetrical subunit of GMP-PCP bound Drp1 lattice on Phosphatidic acid (PA)-containing nanotubes
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.164 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: DNM1L, DLP1, DRP1
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Star
Buffer solutionpH: 7.5
Details: Primary Buffer: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol Nanotubes: 40% D-galactosyl-beta-1-N-nervonyl-erythro-sphingosine (GC), 35% ...Details: Primary Buffer: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol Nanotubes: 40% D-galactosyl-beta-1-N-nervonyl-erythro-sphingosine (GC), 35% phosphatidylethanolamine (PE), 25% phosphatidic acid (PA) Final Sample: Protein diluted to 0.4mg/ml and incubated with 500 uM NTs, 2mM GMPPCP and 2mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2150 mMPotassium chlorideKCl1
35 mMMagnesium dichlorideMgCl21
410 mMBME1
52 mMGMP-PCP1
6500 uMPA Nanotubes1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Drp1 was incubated with nanotubes and GMPPCP to form decorated lipid templates
Specimen supportDetails: 25mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.093 sec. / Electron dose: 58.49 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of real images: 1941
Image scansMovie frames/image: 35

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Processing

EM software
IDNameVersionCategory
2Leginon3.3image acquisition
7MDFFmodel fitting
9RELIONinitial Euler assignment
10cisTEMfinal Euler assignment
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 14.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13215 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 617.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001219634
ELECTRON MICROSCOPYf_angle_d0.329326570
ELECTRON MICROSCOPYf_chiral_restr0.03633176
ELECTRON MICROSCOPYf_plane_restr0.00243426
ELECTRON MICROSCOPYf_dihedral_angle_d6.38277572

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