+Open data
-Basic information
Entry | Database: PDB / ID: 6zh3 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of ESCRT-III helical Vps24 filaments | ||||||
Components | Vacuolar protein-sorting-associated protein 24Vacuole | ||||||
Keywords | LIPID BINDING PROTEIN / Filament / Helical / Membrane Remodeling | ||||||
Function / homology | Function and homology information intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body ...intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Huber, S.T. / Mostafavi, S. / Mortensen, S.A. / Sachse, C. | ||||||
Citation | Journal: Sci Adv / Year: 2020 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zh3.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zh3.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zh3 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zh3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 11212MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10495 (Title: Structure and assembly of ESCRT-III helical Vps24 filaments Data size: 70.0 Data #1: Aligned micrographs of Vps24 helical filaments [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 9
-Components
#1: Protein | Mass: 26562.174 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VPS24, DID3, YKL041W, YKL254 / Production host: Escherichia coli (E. coli) / References: UniProt: P36095 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Doubled-stranded helical filament assembly of Vps24 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES 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 | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Image recording | Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3257 Details: 1320 images were manually selected for further processing |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -32.47 ° / Axial rise/subunit: 25.18 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 524155 / Details: one segment every 24.7 Angstrom | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313554 / Algorithm: BACK PROJECTION / Num. of class averages: 62 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | B value: 126 / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 3FRT Pdb chain-ID: A / Accession code: 3FRT / Source name: PDB / Type: experimental model |