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Yorodumi- EMDB-7958: Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7958 | |||||||||
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Title | Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the membrane in the super constricted state | |||||||||
Map data | Delta-PRD human dynamin 1 assembled on lipid bilayer in the presence of GTP | |||||||||
Sample |
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Keywords | dynamin family / gtpase / pleckstrin homology domain / membrane protein / ENDOCYTOSIS / HYDROLASE | |||||||||
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 / photoreceptor ribbon synapse / Retrograde neurotrophin signalling ...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 / photoreceptor ribbon synapse / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / synaptic vesicle endocytosis / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / receptor-mediated endocytosis / photoreceptor inner segment / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / : / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.1 Å | |||||||||
Authors | Kong L / Wang H | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7958.map.gz | 202.2 MB | EMDB map data format | |
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Header (meta data) | emd-7958-v30.xml emd-7958.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_7958.png | 93.8 KB | ||
Filedesc metadata | emd-7958.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7958 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7958 | HTTPS FTP |
-Related structure data
Related structure data | 6dlvMC 7957C 6dluC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7958.map.gz / Format: CCP4 / Size: 432.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Delta-PRD human dynamin 1 assembled on lipid bilayer in the presence of GTP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GTP-bound human dynamin helical polymer encased around phosphatid...
Entire | Name: GTP-bound human dynamin helical polymer encased around phosphatidylserine lipid bilayer membrane tube |
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Components |
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-Supramolecule #1: GTP-bound human dynamin helical polymer encased around phosphatid...
Supramolecule | Name: GTP-bound human dynamin helical polymer encased around phosphatidylserine lipid bilayer membrane tube type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 98 kDa/nm |
-Macromolecule #1: Dynamin-1
Macromolecule | Name: Dynamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: dynamin GTPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 85.859148 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGKSSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTEY AEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP PDIEFQIRDM L MQFVTKEN ...String: MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGKSSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTEY AEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP PDIEFQIRDM L MQFVTKEN CLILAVSPAN SDLANSDALK VAKEVDPQGQ RTIGVITKLD LMDEGTDARD VLENKLLPLR RGYIGVVNRS QK DIDGKKD ITAALAAERK FFLSHPSYRH LADRMGTPYL QKVLNQQLTN HIRDTLPGLR NKLQSQLLSI EKEVEEYKNF RPD DPARKT KALLQMVQQF AVDFEKRIEG SGDQIDTYEL SGGARINRIF HERFPFELVK MEFDEKELRR EISYAIKNIH GIRT GLFTP DMAFETIVKK QVKKIREPCL KCVDMVISEL ISTVRQCTKK LQQYPRLREE MERIVTTHIR EREGRTKEQV MLLID IELA YMNTNHEDFI GFANAQQRSN QMNKKKTSGN QDEILVIRKG WLTINNIGIM KGGSKEYWFV LTAENLSWYK DDEEKE KKY MLSVDNLKLR DVEKGFMSSK HIFALFNTEQ RNVYKDYRQL ELACETQEEV DSWKASFLRA GVYPERVGDK EKASETE EN GSDSFMHSMD PQLERQVETI RNLVDSYMAI VNKTVRDLMP KTIMHLMINN TKEFIFSELL ANLYSCGDQN TLMEESAE Q AQRRDEMLRM YHALKEALSI IGDINTT UniProtKB: Dynamin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2 |
-Image processing
Startup model | Type of model: NONE / Details: used featureless cylinder as starting model |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 14.63 Å Applied symmetry - Helical parameters - Δ&Phi: 26.14 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14322 |