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- EMDB-6733: Cryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked) -

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Basic information

Entry
Database: EMDB / ID: 6733
TitleCryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked)
SampleVps4-E233Q hexamer
SourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map data
Methodsingle particle reconstruction, at 3.9 Å resolution
AuthorsSun S / Li L
CitationNat Commun, 2017, 8, 16064-16064

Nat Commun, 2017, 8, 16064-16064 Yorodumi Papers
Cryo-EM structures of the ATP-bound Vps4(E233Q) hexamer and its complex with Vta1 at near-atomic resolution.
Shan Sun / Lin Li / Fan Yang / Xiaojing Wang / Fenghui Fan / Mengyi Yang / Chunlai Chen / Xueming Li / Hong-Wei Wang / Sen-Fang Sui

Validation ReportPDB-ID: 5xmi

SummaryFull reportAbout validation report
DateDeposition: May 15, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0539
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0539
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5xmi
  • Surface level: 0.0539
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_6733.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.31 Å/pix.
= 261.308 Å
200 pix
1.31 Å/pix.
= 261.308 Å
200 pix
1.31 Å/pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour Level:0.0539 (by author), 0.0539 (movie #1):
Minimum - Maximum-0.12951745 - 0.25908482
Average (Standard dev.)0.00027270667 (0.00917122)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1300.2590.000

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Supplemental data

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Sample components

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Entire Vps4-E233Q hexamer

EntireName: Vps4-E233Q hexamer / Number of components: 3

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Component #1: cellular-component, Vps4-E233Q hexamer

Cellular-componentName: Vps4-E233Q hexamer / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: strain ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Vacuolar protein sorting-associated protein 4

ProteinName: Vacuolar protein sorting-associated protein 4 / Recombinant expression: No
MassTheoretical: 48.232199 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
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: 50 e/Å2 / Illumination mode: OTHER
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: 106918
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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