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- EMDB-8866: Negative-stain reconstruction of a C-terminal truncation in Ccq1 ... -

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Entry
Database: EMDB / ID: 8866
TitleNegative-stain reconstruction of a C-terminal truncation in Ccq1 of the the S. pombe CTP complex (Ccq1 2-439, Tpz1 406-508, Poz1 2-249)
SampleNegative-stain reconstruction of a C-terminal truncation in Ccq1 of the the S. pombe CTP complex (Ccq1 2-439, Tpz1 406-508, Poz1 2-249)
SourceSchizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /
Map dataNegative-stain reconstruction of a C-terminal truncation in Ccq1 of the the S. pombe CTP complex (Ccq1 2-439, Tpz1 406-508, Poz1 2-249)
Methodsingle particle reconstruction, at 25.9 Å resolution
AuthorsScott HW / Kim JK / Yu C / Huang L / Qiao F / Taylor DJ
CitationJ. Mol. Biol., 2017, 429, 2863-2872

J. Mol. Biol., 2017, 429, 2863-2872 Yorodumi Papers
Spatial Organization and Molecular Interactions of the Schizosaccharomyces pombe Ccq1-Tpz1-Poz1 Shelterin Complex.
Harry Scott / Jin-Kwang Kim / Clinton Yu / Lan Huang / Feng Qiao / Derek J Taylor

DateDeposition: Jul 28, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0867
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0867
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8866.map.gz (map file in CCP4 format, 2371 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
84 pix
3 Å/pix.
= 252.336 Å
84 pix
3 Å/pix.
= 252.336 Å
84 pix
3 Å/pix.
= 252.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.004 Å
Density
Contour Level:0.0867 (by author), 0.0867 (movie #1):
Minimum - Maximum-0.055885047 - 0.28599536
Average (Standard dev.)0.00020288904 (0.01754641)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions848484
Origin000
Limit838383
Spacing848484
CellA=B=C: 252.336 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.0043.0043.004
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z252.336252.336252.336
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS848484
D min/max/mean-0.0560.2860.000

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Supplemental data

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Sample components

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Entire Negative-stain reconstruction of a C-terminal truncation in Ccq1 ...

EntireName: Negative-stain reconstruction of a C-terminal truncation in Ccq1 of the the S. pombe CTP complex (Ccq1 2-439, Tpz1 406-508, Poz1 2-249)
Details: Complex is a dimer of trimers / Number of components: 1

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Component #1: protein, Negative-stain reconstruction of a C-terminal truncation...

ProteinName: Negative-stain reconstruction of a C-terminal truncation in Ccq1 of the the S. pombe CTP complex (Ccq1 2-439, Tpz1 406-508, Poz1 2-249)
Details: Complex is a dimer of trimers / Recombinant expression: No
SourceSpecies: Schizosaccharomyces pombe / yeast / シゾサッカロミセス・ポンベ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.036 mg/ml / pH: 8
Support film15 mA
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: omega in-column
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 15.6 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 2927
3D reconstructionSoftware: RELION / Resolution: 25.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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