+Open data
-Basic information
Entry | Database: PDB / ID: 8t1h | |||||||||
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Title | Cryo-EM structure of a full-length, native Drp1 dimer | |||||||||
Components | Dynamin-1-like protein | |||||||||
Keywords | CYTOSOLIC PROTEIN / Dynamin-related protein 1 / Drp1 / mitochondrial fission / GTPase | |||||||||
Function / homology | Function and homology information mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / Apoptotic execution phase / dynamin GTPase / peroxisome fission / regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / Apoptotic execution phase / dynamin GTPase / peroxisome fission / regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / regulation of mitochondrion organization / positive regulation of mitochondrial fission / heart contraction / intracellular distribution of mitochondria / brush border / necroptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of intrinsic apoptotic signaling pathway / clathrin-coated pit / mitochondrion organization / GTPase activator activity / release of cytochrome c from mitochondria / positive regulation of protein secretion / synaptic vesicle membrane / small GTPase binding / endocytosis / peroxisome / calcium ion transport / rhythmic process / protein complex oligomerization / regulation of gene expression / microtubule binding / protein-containing complex assembly / microtubule / mitochondrial outer membrane / membrane fusion / positive regulation of apoptotic process / intracellular membrane-bounded organelle / GTPase activity / lipid binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.97 Å | |||||||||
Authors | Rochon, K. / Mears, J.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for regulated assembly of the mitochondrial fission GTPase Drp1. Authors: Kristy Rochon / Brianna L Bauer / Nathaniel A Roethler / Yuli Buckley / Chih-Chia Su / Wei Huang / Rajesh Ramachandran / Maria S K Stoll / Edward W Yu / Derek J Taylor / Jason A Mears / Abstract: Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 ...Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 (Drp1) at the surface of mitochondria. As such, Drp1 is essential for inducing mitochondrial division in mammalian cells, and homologous proteins are found in all eukaryotes. As a member of the dynamin superfamily of proteins (DSPs), controlled Drp1 self-assembly into large helical polymers stimulates its GTPase activity to promote membrane constriction. Still, little is known about the mechanisms that regulate correct spatial and temporal assembly of the fission machinery. Here we present a cryo-EM structure of a full-length Drp1 dimer in an auto-inhibited state. This dimer reveals two key conformational rearrangements that must be unlocked through intramolecular rearrangements to achieve the assembly-competent state observed in previous structures. This structural insight provides understanding into the mechanism for regulated self-assembly of the mitochondrial fission machinery. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t1h.cif.gz | 480.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t1h.ent.gz | 332.4 KB | Display | PDB format |
PDBx/mmJSON format | 8t1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t1h_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8t1h_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8t1h_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 8t1h_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/8t1h ftp://data.pdbj.org/pub/pdb/validation_reports/t1/8t1h | HTTPS FTP |
-Related structure data
Related structure data | 40967MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 1 - 736 / Label seq-ID: 1 - 736
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-Components
#1: Protein | Mass: 81984.094 Da / Num. of mol.: 2 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dimer complex of native, full length Drp1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.164 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 Star | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 47.76 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4560 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 883690 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71611 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: 4BEJ Details: Dimer built aligning two AlphaFold Chains to the 4BEJ chains A and B Source name: AlphaFold | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 282.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 1.74629626695E-11 Å |