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Yorodumi- PDB-6dlv: Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the... -
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-Basic information
Entry | Database: PDB / ID: 6dlv | |||||||||
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Title | Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the membrane in the super constricted state | |||||||||
Components | Dynamin-1 | |||||||||
Keywords | ENDOCYTOSIS / HYDROLASE / dynamin family / gtpase / pleckstrin homology domain / membrane protein | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.1 Å | |||||||||
Authors | Kong, L. / Wang, H. / Fang, S. / Canagarajah, B. / Kehr, A.D. / Rice, W.J. / Hinshaw, J.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM of the dynamin polymer assembled on lipid membrane. Authors: Leopold Kong / Kem A Sochacki / Huaibin Wang / Shunming Fang / Bertram Canagarajah / Andrew D Kehr / William J Rice / Marie-Paule Strub / Justin W Taraska / Jenny E Hinshaw / Abstract: Membrane fission is a fundamental process in the regulation and remodelling of cell membranes. Dynamin, a large GTPase, mediates membrane fission by assembling around, constricting and cleaving the ...Membrane fission is a fundamental process in the regulation and remodelling of cell membranes. Dynamin, a large GTPase, mediates membrane fission by assembling around, constricting and cleaving the necks of budding vesicles. Here we report a 3.75 Å resolution cryo-electron microscopy structure of the membrane-associated helical polymer of human dynamin-1 in the GMPPCP-bound state. The structure defines the helical symmetry of the dynamin polymer and the positions of its oligomeric interfaces, which were validated by cell-based endocytosis assays. Compared to the lipid-free tetramer form, membrane-associated dynamin binds to the lipid bilayer with its pleckstrin homology domain (PHD) and self-assembles across the helical rungs via its guanine nucleotide-binding (GTPase) domain. Notably, interaction with the membrane and helical assembly are accommodated by a severely bent bundle signalling element (BSE), which connects the GTPase domain to the rest of the protein. The BSE conformation is asymmetric across the inter-rung GTPase interface, and is unique compared to all known nucleotide-bound states of dynamin. The structure suggests that the BSE bends as a result of forces generated from the GTPase dimer interaction that are transferred across the stalk to the PHD and lipid membrane. Mutations that disrupted the BSE kink impaired endocytosis. We also report a 10.1 Å resolution cryo-electron microscopy map of a super-constricted dynamin polymer showing localized conformational changes at the BSE and GTPase domains, induced by GTP hydrolysis, that drive membrane constriction. Together, our results provide a structural basis for the mechanism of action of dynamin on the lipid membrane. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dlv.cif.gz | 477.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dlv.ent.gz | 400 KB | Display | PDB format |
PDBx/mmJSON format | 6dlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dlv_validation.pdf.gz | 881 KB | Display | wwPDB validaton report |
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Full document | 6dlv_full_validation.pdf.gz | 884.1 KB | Display | |
Data in XML | 6dlv_validation.xml.gz | 67.3 KB | Display | |
Data in CIF | 6dlv_validation.cif.gz | 106.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/6dlv ftp://data.pdbj.org/pub/pdb/validation_reports/dl/6dlv | HTTPS FTP |
-Related structure data
Related structure data | 7958MC 7957C 6dluC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 15 / Rise per n subunits: 14.63 Å / Rotation per n subunits: 26.14 °) |
-Components
#1: Protein | Mass: 85859.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05193, dynamin GTPase |
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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 |
-Sample preparation
Component | Name: GTP-bound human dynamin helical polymer encased around phosphatidylserine lipid bilayer membrane tube Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 98 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 26.14 ° / Axial rise/subunit: 14.63 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14322 / Symmetry type: HELICAL |