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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 / homologyAAA+ ATPase domain / MIT domain superfamily / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / Snf7 family / MIT / Vps4 oligomerisation, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ATPase family associated with various cellular activities (AAA) / Snf7 ...AAA+ ATPase domain / MIT domain superfamily / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / Snf7 family / MIT / Vps4 oligomerisation, C-terminal / P-loop containing nucleoside triphosphate hydrolase / ATPase family associated with various cellular activities (AAA) / Snf7 / MIT (microtubule interacting and transport) domain / Vps4 C terminal oligomerisation domain / AAA-protein family signature. / Macroautophagy / Lysosome Vesicle Biogenesis / ESCRT IV complex / ESCRT III complex / ATP export / intralumenal vesicle formation / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / sterol metabolic process / macroautophagy / protein transport / protein homooligomerization / ATPase activity / endosome / protein homodimerization activity / membrane / ATP binding / identical protein binding / nucleus / cytoplasm / DOA4-independent degradation protein 4 / Vacuolar protein sorting-associated protein 4
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2017 / Release: Dec 6, 2017

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Structure visualization

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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
Polyers186,5586
Non-polymers2,43112
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21770
ΔGint (kcal/M)-108
Surface area (Å2)61180

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Components

#1: Protein/peptide
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: (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: (synth.) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P36108*PLUS
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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
MicroscopyMicroscope model: 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
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 82225 / Symmetry type: POINT
Least-squares processHighest resolution: 3.2 Å
Refine LS restraints
Refine 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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