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- EMDB-40946: Cryo-EM of the GDP-bound human dynamin (full-length) polymer asse... -
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Open data
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Basic information
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Title | Cryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix) | ||||||||||||
![]() | GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix) | ||||||||||||
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Function / homology | ![]() clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | helical reconstruction / ![]() | ||||||||||||
![]() | Jimah JR / Canagarajah BJ / Hinshaw JE | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Authors: John R Jimah / Nidhi Kundu / Abigail E Stanton / Kem A Sochacki / Bertram Canagarajah / Lieza Chan / Marie-Paule Strub / Huaibin Wang / Justin W Taraska / Jenny E Hinshaw / ![]() Abstract: Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the ...Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 51.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.6 KB | Display | ![]() |
Images | ![]() | 113.7 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 442 MB 442 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t0rMC ![]() 8sxzC ![]() 8sz4C ![]() 8sz7C ![]() 8sz8C ![]() 8t0kC ![]() 8tymC ![]() 8tynC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state (full helix) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.289 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: Half Map 1
File | emd_40946_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
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Density Histograms |
-Half map: Half Map 2
File | emd_40946_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : GDP-bound human dynamin (full-length) helical polymer assembled o...
Entire | Name: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix) |
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Components |
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-Supramolecule #1: GDP-bound human dynamin (full-length) helical polymer assembled o...
Supramolecule | Name: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane (full helix) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 98.7 kDa/nm |
-Macromolecule #1: Dynamin-1
Macromolecule | Name: Dynamin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 98.825742 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAHHHHHHTG MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGASSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTE YAEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP P DIEFQIRD ...String: MAHHHHHHTG MGNRGMEDLI PLVNRLQDAF SAIGQNADLD LPQIAVVGGQ SAGASSVLEN FVGRDFLPRG SGIVTRRPLV LQLVNATTE YAEFLHCKGK KFTDFEEVRL EIEAETDRVT GTNKGISPVP INLRVYSPHV LNLTLVDLPG MTKVPVGDQP P DIEFQIRD MLMQFVTKEN CLILAVSPAN SDLANSDALK VAKEVDPQGQ RTIGVITKLD LMDEGTDARD VLENKLLPLR RG YIGVVNR SQKDIDGKKD ITAALAAERK FFLSHPSYRH LADRMGTPYL QKVLNQQLTN HIRDTLPGLR NKLQSQLLSI EKE VEEYKN FRPDDPARKT KALLQMVQQF AVDFEKRIEG SGDQIDTYEL SGGARINRIF HERFPFELVK MEFDEKELRR EISY AIKNI HGIRTGLFTP DMAFETIVKK QVKKIREPCL KCVDMVISEL ISTVRQCTKK LQQYPRLREE MERIVTTHIR EREGR TKEQ VMLLIDIELA YMNTNHEDFI GFANAQQRSN QMNKKKTSGN QDEILVIRKG WLTINNIGIM KGGSKEYWFV LTAENL SWY KDDEEKEKKY MLSVDNLKLR DVEKGFMSSK HIFALFNTEQ RNVYKDYRQL ELACETQEEV DSWKASFLRA GVYPERV GD KEKASETEEN GSDSFMHSMD PQLERQVETI RNLVDSYMAI VNKTVRDLMP KTIMHLMINN TKEFIFSELL ANLYSCGD Q NTLMEESAEQ AQRRDEMLRM YHALKEALSI IGNINTTTVS TPMPPPVDDS WLQVQSVPAG RRSPTSSPTP QRRAPAVPP ARPGSRGPAP GPPPAGSALG GAPPVPSRPG ASPDPFGPPP QVPSRPNRAP PGVPSRSGQA SPSRPESPRP PFDLGT UniProtKB: ![]() |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |