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- EMDB-8892: Focused classification map for VSL dimer bridging Subunit B and C... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8892 | |||||||||
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Title | Focused classification map for VSL dimer bridging Subunit B and C of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p | |||||||||
![]() | Vps4-Vta1 complex | |||||||||
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Function / homology | ![]() ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vacuole organization / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / lipid transport / reticulophagy / endosomal transport / ATPase complex / nucleus organization / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / protein-macromolecule adaptor activity / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Han H / Monroe N | |||||||||
![]() | ![]() Title: The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Authors: Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill / ![]() Abstract: The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now ...The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a 'conveyor belt' model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end. | |||||||||
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 | ![]() | 49.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 102.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.2 KB | Display | ![]() |
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Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8887C ![]() 8888C ![]() 8889C ![]() 8890C ![]() 8891C ![]() 8893C ![]() 8894C ![]() 8895C ![]() 8896C ![]() 6ap1C ![]() 6bmfC C: citing same article ( |
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Similar structure data |
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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 | Vps4-Vta1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Vps4-Vta1 complex
Entire | Name: Vps4-Vta1 complex |
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Components |
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-Supramolecule #1: Vps4-Vta1 complex
Supramolecule | Name: Vps4-Vta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
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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 / Average exposure time: 0.25 sec. / Average electron dose: 1.55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL / Details: e2initialmodel.py |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 65944 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |