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- EMDB-8889: Focused classification map for high position subunit F of Vps4p-V... -

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Basic information

Entry
Database: EMDB / ID: 8889
TitleFocused classification map for high position subunit F of Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p
SampleVps4-Vta1 complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataVps4-Vta1 complex
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsHan H / Monroe N
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill

DateDeposition: Aug 17, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0197
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0197
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8889.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.1 Å/pix.
= 280.602 Å
256 pix
1.1 Å/pix.
= 280.602 Å
256 pix
1.1 Å/pix.
= 280.602 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.0961 Å
Density
Contour Level:0.0197 (by author), 0.0197 (movie #1):
Minimum - Maximum-0.02111671 - 0.06198096
Average (Standard dev.)-0.00023016865 (0.0023693042)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 280.6016 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09610156251.09610156251.0961015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z280.602280.602280.602
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0210.062-0.000

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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: 1

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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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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: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.55 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: 21459
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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