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- EMDB-2701: Human dynamin 1 K44A superconstricted polymer stabilized with GTP -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2701 | |||||||||
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Title | Human dynamin 1 K44A superconstricted polymer stabilized with GTP | |||||||||
![]() | Reconstruction of a dynamin mutant, K44A, bound to DOPS lipid tube | |||||||||
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![]() | Dynamin / endocytosis / membrane fission / GTPase / intracellular trafficking | |||||||||
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 | helical reconstruction / cryo EM / Resolution: 12.5 Å | |||||||||
![]() | Sundborger AC / Fang S / Heymann JA / Ray P / Chappie JS / Hinshaw JE | |||||||||
![]() | ![]() Title: A dynamin mutant defines a superconstricted prefission state. Authors: Anna C Sundborger / Shunming Fang / Jürgen A Heymann / Pampa Ray / Joshua S Chappie / Jenny E Hinshaw / ![]() Abstract: Dynamin is a 100 kDa GTPase that organizes into helical assemblies at the base of nascent clathrin-coated vesicles. Formation of these oligomers stimulates the intrinsic GTPase activity of dynamin, ...Dynamin is a 100 kDa GTPase that organizes into helical assemblies at the base of nascent clathrin-coated vesicles. Formation of these oligomers stimulates the intrinsic GTPase activity of dynamin, which is necessary for efficient membrane fission during endocytosis. Recent evidence suggests that the transition state of dynamin's GTP hydrolysis reaction serves as a key determinant of productive fission. Here, we present the structure of a transition-state-defective dynamin mutant K44A trapped in a prefission state at 12.5 Å resolution. This structure constricts to 3.7 nm, reaching the theoretical limit required for spontaneous membrane fission. Computational docking indicates that the ground-state conformation of the dynamin polymer is sufficient to achieve this superconstricted prefission state and reveals how a two-start helical symmetry promotes the most efficient packing of dynamin tetramers around the membrane neck. These data suggest a model for the assembly and regulation of the minimal dynamin fission machine. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
Images | ![]() | 194.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uudMC ![]() 4uukMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of a dynamin mutant, K44A, bound to DOPS lipid tube | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.55 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : GTP-stablized human dynamin 1 K44A dynamin polymer bound to DOPS ...
Entire | Name: GTP-stablized human dynamin 1 K44A dynamin polymer bound to DOPS lipid bilayer |
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Components |
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-Supramolecule #1000: GTP-stablized human dynamin 1 K44A dynamin polymer bound to DOPS ...
Supramolecule | Name: GTP-stablized human dynamin 1 K44A dynamin polymer bound to DOPS lipid bilayer type: sample / ID: 1000 / Oligomeric state: helical assembly of dynamin / Number unique components: 1 |
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-Macromolecule #1: Human dynamin 1
Macromolecule | Name: Human dynamin 1 / type: protein_or_peptide / ID: 1 / Oligomeric state: helical assembly / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 98 MDa / Theoretical: 97.3 MDa |
Recombinant expression | Organism: ![]() ![]() Recombinant plasmid: pBlueBacIII baculovirus expression vector |
Sequence | UniProtKB: Dynamin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.2 Details: 20 mM Hepes, 150 mM NaCl, 1 mM EGTA, 1 mM DTT, 1 mM MgCl |
Grid | Details: Quantifoil R3.5/1 200 mesh Cu Holey Carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: 40 seconds pre-blot, 2 second blot before plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 93 K / Max: 95 K / Average: 94 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Dec 17, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.5 µm / Number real images: 357 / Average electron dose: 10 e/Å2 / Od range: 1.5 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 49000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 49000 |
Sample stage | Specimen holder: Liquid Nitrogen cooled / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | The particles were aligned using IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 17.19 Å Applied symmetry - Helical parameters - Δ&Phi: 30.59 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: OTHER / Software - Name: Spider Details: A total of 7525 helical segments were incorporated by the IHRSR algorithm into the final reconstruction after 50 cycles |
CTF correction | Details: each image using bsoft |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: YUP |
Details | Initial fitting was performed using GG-GMPPCP monomers (PDB: 3ZYC), dynamin middle/GED stalk monomers excised from (PDB: 3SNH), and PH domain monomers (PDB: 1DYN). All-atom structures were refined using the YUP.SCX method of the YUP software package. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-4uud: ![]() PDB-4uuk: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: YUP |
Details | Initial fitting was performed using GG-GMPPCP monomers (PDB: 3ZYC), dynamin middle/GED stalk monomers excised from (PDB: 3SNH), and PH domain monomers (PDB: 1DYN). All-atom structures were refined using the YUP.SCX method of the YUP software package. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-4uud: ![]() PDB-4uuk: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: YUP |
Details | Initial fitting was performed using GG-GMPPCP monomers (PDB: 3ZYC), dynamin middle/GED stalk monomers excised from (PDB: 3SNH), and PH domain monomers (PDB: 1DYN). All-atom structures were refined using the YUP.SCX method of the YUP software package. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-4uud: ![]() PDB-4uuk: |