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- EMDB-8553: Vps4-Vta1 complex, VSL_B -

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Basic information

Database: EMDB / ID: 8553
TitleVps4-Vta1 complex, VSL_B
SampleVps4-vta1 complex
SourceSaccharomyces cerevisiae / yeast / /
Map dataVps4-Vta1 complex, VSL_B
Methodsingle particle reconstruction, at 6.7 Å resolution
AuthorsMonroe N / Shen P / Han H / Sundquist WI / Hill CP
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.
Nicole Monroe / Han Han / Peter S Shen / Wesley I Sundquist / Christopher P Hill

DateDeposition: Jan 13, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Apr 12, 2017 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_8553.map.gz (map file in CCP4 format, 10513 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.409 Å
Contour Level:0.0253 (by author), 0.022 (movie #1):
Minimum - Maximum-0.018700633 - 0.05690021
Average (Standard dev.)-0.0008448647 (0.0053864163)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0190.057-0.001

Supplemental data

Sample components

Entire Vps4-vta1 complex

EntireName: Vps4-vta1 complex / Number of components: 4

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

Component #2: protein, Vps4p

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

Component #3: protein, Vps2p

ProteinName: Vps2p / Recombinant expression: No

Component #4: protein, Vta1p

ProteinName: Vta1p / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / /

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 80 %

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)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 38421
3D reconstructionSoftware: RELION / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF

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