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Yorodumi- PDB-6bmf: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bmf | ||||||
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Title | Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase | ||||||
Function / homology | Function and homology information Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / endosome transport via multivesicular body sorting pathway ...Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / protein retention in Golgi apparatus / ESCRT III complex / 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 / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / reticulophagy / nucleus organization / endosomal transport / ATPase complex / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Han, H. / Monroe, N. / Shen, P. / Sundquist, W.I. / Hill, C.P. | ||||||
Citation | Journal: Elife / Year: 2017 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bmf.cif.gz | 248 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bmf.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bmf ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bmf | HTTPS FTP |
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-Related structure data
Related structure data | 8887MC 8888C 8889C 8890C 8891C 8892C 8893C 8894C 8895C 8896C 6ap1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 37120.750 Da / Num. of mol.: 5 / Fragment: UNP residues 101-437 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52917 #2: Protein/peptide | | Mass: 954.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36108*PLUS #3: Chemical | ChemComp-ADP / #4: Chemical | #5: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Vps4p-Vps2p complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 1.55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 / Used frames/image: 2-40 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82225 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.2 Å | ||||||||||||||||||||||||
Refine LS restraints |
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