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- PDB-8t1h: Cryo-EM structure of a full-length, native Drp1 dimer -

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Basic information

Entry
Database: PDB / ID: 8t1h
TitleCryo-EM structure of a full-length, native Drp1 dimer
ComponentsDynamin-1-like protein
KeywordsCYTOSOLIC 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 / intracellular distribution of mitochondria / heart contraction / 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 / microtubule binding / regulation of gene expression / 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
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: 5.97 Å
AuthorsRochon, K. / Mears, J.A.
Funding support United States, 2items
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)F31 GM139324 United States
CitationJournal: 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
DepositionJun 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,9682
Polymers163,9682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

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

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

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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: 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

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Experiment

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

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Sample preparation

ComponentName: Dimer complex of native, full length Drp1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.164 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Star
Buffer solutionpH: 7.5
Details: 25 mM HEPES (KOH) pH 7.5, 0.15 M KCl, 5 mM MgCl2, 10 mM Beta-mercaptoethanol
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2150 mMKCl1
35 mMMgCl21
410 mMBME1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 47.76 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4560

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selectionIntegrated into cryoSPARC
4cryoSPARC3CTF correctionPatch CTF
7UCSF Chimera1.13model fittingRigid Body Docking
8MDFFmodel fitting
10cryoSPARC3initial Euler assignment
11cryoSPARC3final Euler assignment
12cryoSPARC3classification
13cryoSPARC33D reconstruction
20PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 883690
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71611 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingAccession code: 4BEJ
Details: Dimer built aligning two AlphaFold Chains to the 4BEJ chains A and B
Source name: AlphaFold
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 282.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00149544
ELECTRON MICROSCOPYf_angle_d0.34912922
ELECTRON MICROSCOPYf_chiral_restr0.03661548
ELECTRON MICROSCOPYf_plane_restr0.00251662
ELECTRON MICROSCOPYf_dihedral_angle_d7.66813668
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.74629626695E-11 Å

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