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- EMDB-40903: Cryo-EM of the GDP-bound human dynamin polymer assembled on the m... -
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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 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 | ![]() | 57.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.6 KB | Display | ![]() |
Images | ![]() | 99.9 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 442 MB 442 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sz8MC ![]() 8sxzC ![]() 8sz4C ![]() 8sz7C ![]() 8t0kC ![]() 8t0rC ![]() 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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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: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : Cryo-EM of the GDP-bound human dynamin polymer assembled on the m...
Entire | Name: Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state (full helix) |
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Components |
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-Supramolecule #1: Cryo-EM of the GDP-bound human dynamin polymer assembled on the m...
Supramolecule | Name: Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state (full helix) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 85.7 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: 86.312625 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: GPTGMGNRGM EDLIPLVNRL QDAFSAIGQN ADLDLPQIAV VGGQSAGASS VLENFVGRDF LPRGSGIVTR RPLVLQLVNA TTEYAEFLH CKGKKFTDFE EVRLEIEAET DRVTGTNKGI SPVPINLRVY SPHVLNLTLV DLPGMTKVPV GDQPPDIEFQ I RDMLMQFV ...String: GPTGMGNRGM EDLIPLVNRL QDAFSAIGQN ADLDLPQIAV VGGQSAGASS VLENFVGRDF LPRGSGIVTR RPLVLQLVNA TTEYAEFLH CKGKKFTDFE EVRLEIEAET DRVTGTNKGI SPVPINLRVY SPHVLNLTLV DLPGMTKVPV GDQPPDIEFQ I RDMLMQFV TKENCLILAV SPANSDLANS DALKVAKEVD PQGQRTIGVI TKLDLMDEGT DARDVLENKL LPLRRGYIGV VN RSQKDID GKKDITAALA AERKFFLSHP SYRHLADRMG TPYLQKVLNQ QLTNHIRDTL PGLRNKLQSQ LLSIEKEVEE YKN FRPDDP ARKTKALLQM VQQFAVDFEK RIEGSGDQID TYELSGGARI NRIFHERFPF ELVKMEFDEK ELRREISYAI KNIH GIRTG LFTPDMAFET IVKKQVKKIR EPCLKCVDMV ISELISTVRQ CTKKLQQYPR LREEMERIVT THIREREGRT KEQVM LLID IELAYMNTNH EDFIGFANAQ QRSNQMNKKK TSGNQDEILV IRKGWLTINN IGIMKGGSKE YWFVLTAENL SWYKDD EEK EKKYMLSVDN LKLRDVEKGF MSSKHIFALF NTEQRNVYKD YRQLELACET QEEVDSWKAS FLRAGVYPER VGDKEKA SE TEENGSDSFM HSMDPQLERQ VETIRNLVDS YMAIVNKTVR DLMPKTIMHL MINNTKEFIF SELLANLYSC GDQNTLME E SAEQAQRRDE MLRMYHALKE ALSIIGNINT TTV 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 |