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- EMDB-8550: Vps4-Vta1 complex, sharpened map -

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Basic information

Entry
Database: EMDB / ID: 8550
TitleVps4-Vta1 complex, sharpened map
Map dataVps4-Vta1 complex, sharpened map
SampleVps4-Vta1 complex
  • Vps4p
  • Vta1
  • Vps2p
Function/homologyVacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / ESCRT IV complex / intralumenal vesicle formation / protein retention in Golgi apparatus / MIT / late endosome to vacuole transport via multivesicular body sorting pathway / MIT domain superfamily / vacuole organization / MIT (microtubule interacting and transport) domain / late endosome to vacuole transport ...Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / ESCRT IV complex / intralumenal vesicle formation / protein retention in Golgi apparatus / MIT / late endosome to vacuole transport via multivesicular body sorting pathway / MIT domain superfamily / vacuole organization / MIT (microtubule interacting and transport) domain / late endosome to vacuole transport / ATPase activator activity / Vps4 oligomerisation, C-terminal / sterol metabolic process / Vps4 C terminal oligomerisation domain / lipid transport / ATPase, AAA-type, conserved site / AAA-protein family signature. / positive regulation of protein oligomerization / ATPase, AAA-type, core / multivesicular body / ATPase family associated with various cellular activities (AAA) / macroautophagy / protein transport / protein homooligomerization / ATPase activity / AAA+ ATPase domain / endosome / protein homodimerization activity / P-loop containing nucleoside triphosphate hydrolase / membrane / ATP binding / identical protein binding / nucleus / | / Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1
Function and homology information
SourceSaccharomyces cerevisiae / / yeast /
MethodCryo EM / single particle reconstruction / 4.3 Å resolution
AuthorsMonroe N / Shen P / Han H / Sundquist WI / Hill CP
CitationJournal: Elife / Year: 2017
Title: Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.
Authors: Nicole Monroe / Han Han / Peter S Shen / Wesley I Sundquist / Christopher P Hill
Abstract: Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM ...Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeF, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 'walks' along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases.
DateDeposition: Jan 13, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Apr 12, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0674
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0674
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8550.map.gz (map file in CCP4 format, 10513 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
138 pix
1.41 Å/pix.
= 194.442 Å
138 pix
1.41 Å/pix.
= 194.442 Å
138 pix
1.41 Å/pix.
= 194.442 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.409 Å
Density
Contour Level:0.0674 (by author), 0.0674 (movie #1):
Minimum - Maximum-0.09996606 - 0.24436772
Average (Standard dev.)0.002470805 (0.013176317)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions138138138
Origin000
Limit137137137
Spacing138138138
CellA=B=C: 194.442 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4091.4091.409
M x/y/z138138138
origin x/y/z0.0000.0000.000
length x/y/z194.442194.442194.442
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.1000.2440.002

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Supplemental data

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Sample components

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Entire Vps4-Vta1 complex

EntireName: Vps4-Vta1 complex / Number of components: 4

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Component #1: protein, Vps4-Vta1 complex

ProteinName: Vps4-Vta1 complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / / yeast /
Source (engineered)Expression System: Escherichia coli bl21(de3) / / bacteria / image: Escherichia coli

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Component #2: protein, Vps4p

ProteinName: Vps4p / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae / / yeast /

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Component #3: protein, Vta1

ProteinName: Vta1 / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae / / yeast /

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Component #4: protein, Vps2p

ProteinName: Vps2p / Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 588155
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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