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- PDB-7ax3: CryoEM structure of the super-constricted two-start dynamin 1 filament -
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Basic information
Entry | Database: PDB / ID: 7ax3 | ||||||
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Title | CryoEM structure of the super-constricted two-start dynamin 1 filament | ||||||
![]() | Dynamin-1 | ||||||
![]() | CYTOSOLIC PROTEIN / DYNAMIN | ||||||
Function / homology | ![]() clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / endosome organization ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / endosome organization / Formation of annular gap junctions / photoreceptor ribbon synapse / Gap junction degradation / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / Clathrin-mediated endocytosis / presynapse / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.74 Å | ||||||
![]() | Liu, J.W. / Zhang, P.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of the super-constricted two-start dynamin 1 filament. Authors: Jiwei Liu / Frances Joan D Alvarez / Daniel K Clare / Jeffrey K Noel / Peijun Zhang / ![]() ![]() ![]() Abstract: Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical ...Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.7 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11932MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 97536.359 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-GCP / #3: Chemical | ChemComp-MG / 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: dynamin 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7 |
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 |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 24.43 ° / Axial rise/subunit: 13.58 Å / Axial symmetry: C2 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16772 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.05 Å2 | ||||||||||||||||||||||||
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