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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11212 | |||||||||
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Title | Cryo-EM structure of ESCRT-III helical Vps24 filaments | |||||||||
![]() | Sharpened cryo EM density | |||||||||
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![]() | Filament / Helical / Membrane Remodeling / LIPID BINDING PROTEIN | |||||||||
Function / homology | ![]() Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / ATP export / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body ...Sealing of the nuclear envelope (NE) by ESCRT-III / intralumenal vesicle formation / Macroautophagy / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / ATP export / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body / protein transport / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Huber ST / Mostafavi S | |||||||||
![]() | ![]() Title: Structure and assembly of ESCRT-III helical Vps24 filaments. Authors: Stefan T Huber / Siavash Mostafavi / Simon A Mortensen / Carsten Sachse / ![]() Abstract: ESCRT-III proteins mediate a range of cellular membrane remodeling activities such as multivesicular body biogenesis, cytokinesis, and viral release. Critical to these processes is the assembly of ...ESCRT-III proteins mediate a range of cellular membrane remodeling activities such as multivesicular body biogenesis, cytokinesis, and viral release. Critical to these processes is the assembly of ESCRT-III subunits into polymeric structures. In this study, we determined the cryo-EM structure of a helical assembly of Vps24 at 3.2-Å resolution and found that Vps24 adopts an elongated open conformation. Vps24 forms a domain-swapped dimer extended into protofilaments that associate into a double-stranded apolar filament. We demonstrate that, upon binding negatively charged lipids, Vps24 homopolymer filaments undergo partial disassembly into shorter filament fragments and oligomers. Upon the addition of Vps24, Vps2, and Snf7, liposomes are deformed into neck and tubular structures by an ESCRT-III heteropolymer coat. The filamentous Vps24 homopolymer assembly structure and interaction studies reveal how Vps24 could introduce unique geometric properties to mixed-type ESCRT-III heteropolymers and contribute to the process of membrane scission events. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 19.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 204.5 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() | 19.2 MB 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zh3MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 70.0 Data #1: Aligned micrographs of Vps24 helical filaments [micrographs - single frame]) |
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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 | Sharpened cryo EM density | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened cryo EM density
File | emd_11212_additional.map | ||||||||||||
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Annotation | Unsharpened cryo EM density | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_11212_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_11212_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Doubled-stranded helical filament assembly of Vps24
Entire | Name: Doubled-stranded helical filament assembly of Vps24 |
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Components |
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-Supramolecule #1: Doubled-stranded helical filament assembly of Vps24
Supramolecule | Name: Doubled-stranded helical filament assembly of Vps24 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Vacuolar protein-sorting-associated protein 24
Macromolecule | Name: Vacuolar protein-sorting-associated protein 24 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 26.562174 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMDYIKKA IWGPDPKEQQ RRIRSVLRKN GRNIEKSLRE LTVLQNKTQQ LIKKSAKKND VRTVRLYAKE LYQINKQYDR MYTSRAQLD SVRMKIDEAI RMNTLSNQMA DSAGLMREVN SLVRLPQLRN TMIELEKELM KSGIISEMVD DTMESVGDVG E EMDEAVDE ...String: GSHMDYIKKA IWGPDPKEQQ RRIRSVLRKN GRNIEKSLRE LTVLQNKTQQ LIKKSAKKND VRTVRLYAKE LYQINKQYDR MYTSRAQLD SVRMKIDEAI RMNTLSNQMA DSAGLMREVN SLVRLPQLRN TMIELEKELM KSGIISEMVD DTMESVGDVG E EMDEAVDE EVNKIVEQYT NEKFKNVDQV PTVELAANEE EQEIPDEKVD EEADRMVNEM RERLRALQN UniProtKB: Vacuolar protein-sorting-associated protein 24 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.9 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | Sample was concentrated to 5 mg/mL, incubated in the refridgerator overnight, ultracentrifugated, and resuspended to a final concentration of 0.9 mg/mL for cryo-EM |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number real images: 3257 / Average electron dose: 1.0 e/Å2 Details: 1320 images were manually selected for further processing |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |