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- PDB-6bmf: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -

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Basic information

Entry
Database: PDB / ID: 6bmf
TitleVps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Components
  • Vacuolar protein sorting-associated protein 4Vacuole
  • Vps2p
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Function / homology
Function and homology information


ESCRT IV complex / ESCRT III complex / intralumenal vesicle formation / endosome transport via multivesicular body sorting pathway / ATP export / protein retention in Golgi apparatus / vacuole organization / late endosome to vacuole transport via multivesicular body sorting pathway / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport ...ESCRT IV complex / ESCRT III complex / intralumenal vesicle formation / endosome transport via multivesicular body sorting pathway / ATP export / protein retention in Golgi apparatus / vacuole organization / late endosome to vacuole transport via multivesicular body sorting pathway / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport / sterol metabolic process / reticulophagy / multivesicular body / macroautophagy / protein transport / endosome / ATPase activity / endoplasmic reticulum / protein homodimerization activity / membrane / ATP binding / identical protein binding / nucleus / cytoplasm
Snf7 family / ATPase, AAA-type, conserved site / Vps4 C terminal oligomerisation domain / ATPase family associated with various cellular activities (AAA) / Vacuolar protein sorting-associated protein IST1-like / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / AAA+ ATPase domain ...Snf7 family / ATPase, AAA-type, conserved site / Vps4 C terminal oligomerisation domain / ATPase family associated with various cellular activities (AAA) / Vacuolar protein sorting-associated protein IST1-like / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / AAA+ ATPase domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
DOA4-independent degradation protein 4 / Vacuolar protein sorting-associated protein 4
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHan, H. / Monroe, N. / Shen, P. / Sundquist, W.I. / Hill, C.P.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4
B: Vacuolar protein sorting-associated protein 4
C: Vacuolar protein sorting-associated protein 4
D: Vacuolar protein sorting-associated protein 4
E: Vacuolar protein sorting-associated protein 4
G: Vps2p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,98918
Polymers186,5586
Non-polymers2,43112
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21770 Å2
ΔGint-108 kcal/mol
Surface area61180 Å2

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Components

#1: Protein
Vacuolar protein sorting-associated protein 4 / Vacuole / Vps4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10


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 (baker'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 Vps2p


Mass: 954.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36108*PLUS
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vps4p-Vps2p complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 2-40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategory
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82225 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01812700
ELECTRON MICROSCOPYf_angle_d1.55317171
ELECTRON MICROSCOPYf_dihedral_angle_d5.9137740
ELECTRON MICROSCOPYf_chiral_restr0.0781949
ELECTRON MICROSCOPYf_plane_restr0.0112197

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