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- EMDB-8555: Vps4-Vta1 complex, VSL_D -

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Basic information

Entry
Database: EMDB / ID: 8555
TitleVps4-Vta1 complex, VSL_D
SampleVps4-vta1 complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataVps4-Vta1 complex, VSL_D
Methodsingle particle reconstruction, at 6.9 Å resolution
AuthorsMonroe N / Shen P / Han H / Sundquist WI / Hill CP
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
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: Jan 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8555.map.gz (map file in CCP4 format, 10513 KB)
Projections & slices

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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:0.0068 (by author), 0.018 (movie #1):
Minimum - Maximum-0.018346062 - 0.05847411
Average (Standard dev.)-0.00083730795 (0.0052697165)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions138138138
Origin000
Limit137137137
Spacing138138138
CellA=B=C: 194.442 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.0180.058-0.001

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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 / サッカロミセス・セレビシエ /
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 / サッカロミセス・セレビシエ /

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Component #3: protein, Vta1p

ProteinName: Vta1p / Recombinant expression: No
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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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

Specimen stateparticle
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 / Number of projections: 38421
3D reconstructionSoftware: relion / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF

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