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- EMDB-8587: AAA ATPase Vps4 hexamer in closed conformation -

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Basic information

Entry
Database: EMDB / ID: 8587
TitleAAA ATPase Vps4 hexamer in closed conformation
Map dataAAA ATPase Vps4 hexamer in closed conformation
SampleVps4:
Function / homologyATPase family associated with various cellular activities (AAA) / MIT (microtubule interacting and transport) domain / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / AAA-protein family signature. ...ATPase family associated with various cellular activities (AAA) / MIT (microtubule interacting and transport) domain / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / AAA-protein family signature. / Vps4 C terminal oligomerisation domain / ESCRT IV complex / intralumenal vesicle formation / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / sterol metabolic process / macroautophagy / protein transport / protein homooligomerization / ATPase activity / endosome / protein homodimerization activity / membrane / ATP binding / identical protein binding / nucleus / Vacuolar protein sorting-associated protein 4
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 6 Å resolution
AuthorsSu M / Guo EZ
CitationJournal: Sci Adv / Year: 2017
Title: Mechanism of Vps4 hexamer function revealed by cryo-EM.
Authors: Min Su / Emily Z Guo / Xinqiang Ding / Yan Li / Jeffrey T Tarrasch / Charles L Brooks / Zhaohui Xu / Georgios Skiniotis
DateDeposition: Feb 3, 2017 / Header (metadata) release: Mar 8, 2017 / Map release: Nov 8, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8587.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2 Å/pix.
= 256. Å
128 pix
2 Å/pix.
= 256. Å
128 pix
2 Å/pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.28010008 - 0.49596047
Average (Standard dev.)0.001731898 (0.018840462)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 256 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2800.4960.002

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Supplemental data

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Sample components

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Entire Vps4

EntireName: Vps4 / Number of components: 2

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Component #1: protein, Vps4

ProteinName: Vps4 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Vps4

ProteinName: Vps4 / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 99175
3D reconstructionSoftware: RELION / Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF

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