[English] 日本語
![](img/lk-miru.gif)
- EMDB-40902: Cryo-EM of the GDP-bound human dynamin polymer assembled on the m... -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state showing the second PH domain | ||||||||||||
![]() | GDP-bound human dynamin polymer assembled on the membrane in the super constricted state showing the second PH domain | ||||||||||||
![]() |
| ||||||||||||
![]() | dynamin / membrane / fission / lipid / tubule / scission / endocytosis / HYDROLASE | ||||||||||||
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: 2.84 Å | ||||||||||||
![]() | Jimah JR / Canagarajah BJ / Hinshaw JE | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 685 KB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.4 KB | Display | ![]() |
Images | ![]() | 43.5 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 441.7 MB 441.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sz7MC ![]() 8sxzC ![]() 8sz4C ![]() 8sz8C ![]() 8t0kC ![]() 8t0rC ![]() 8tymC ![]() 8tynC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | GDP-bound human dynamin polymer assembled on the membrane in the super constricted state showing the second PH domain | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.289 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 1
File | emd_40902_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 2
File | emd_40902_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : GDP-bound human dynamin helical polymer assembled on the membrane
Entire | Name: GDP-bound human dynamin helical polymer assembled on the membrane |
---|---|
Components |
|
-Supramolecule #1: GDP-bound human dynamin helical polymer assembled on the membrane
Supramolecule | Name: GDP-bound human dynamin helical polymer assembled on the membrane type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
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: 1 / Enantiomer: LEVO / EC number: dynamin GTPase |
---|---|
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: Dynamin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | helical reconstruction |
Aggregation state | filament |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |