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- EMDB-8863: Negative-stain reconstruction of the S. pombe CTP complex (Ccq1 2... -

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Basic information

Entry
Database: EMDB / ID: 8863
TitleNegative-stain reconstruction of the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249)
Map dataNegative-stain reconstruction of the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249).
SampleS. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249) as a dimer of trimers:
Function / homologyAdrenocortical dysplasia protein / meiotic spindle pole body / negative regulation of DNA recombination at telomere / telomere-telomerase complex assembly / positive regulation of single-stranded telomeric DNA binding / protein binding involved in negative regulation of telomere maintenance via telomerase / telomere assembly / telomeric heterochromatin / meiotic telomere clustering / positive regulation of telomere maintenance ...Adrenocortical dysplasia protein / meiotic spindle pole body / negative regulation of DNA recombination at telomere / telomere-telomerase complex assembly / positive regulation of single-stranded telomeric DNA binding / protein binding involved in negative regulation of telomere maintenance via telomerase / telomere assembly / telomeric heterochromatin / meiotic telomere clustering / positive regulation of telomere maintenance / meiotic chromosome segregation / telomere cap complex / mitotic telomere maintenance via semi-conservative replication / nuclear telomeric heterochromatin / shelterin complex / negative regulation of telomere maintenance via telomerase / chromatin silencing at telomere / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere capping / protection from non-homologous end joining at telomere / cellular protein localization / telomere organization / DNA polymerase binding / negative regulation of telomerase activity / telomere maintenance / positive regulation of telomere maintenance via telomerase / positive regulation of telomerase activity / nuclear chromosome, telomeric region / nuclear body / protein-containing complex binding / DNA binding / nucleoplasm / nucleus / cytosol / Protection of telomeres protein poz1 / Protection of telomeres protein tpz1 / Coiled-coil quantitatively-enriched protein 1
Function and homology information
SourceSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / 34.4 Å resolution
AuthorsScott HW / Kim JK / Yu C / Huang L / Qiao F / Taylor DJ
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Spatial Organization and Molecular Interactions of the Schizosaccharomyces pombe Ccq1-Tpz1-Poz1 Shelterin Complex.
Authors: Harry Scott / Jin-Kwang Kim / Clinton Yu / Lan Huang / Feng Qiao / Derek J Taylor
Abstract: The shelterin complex is a macromolecular assembly of proteins that binds to and protects telomeric DNA, which composes the ends of all linear chromosomes. Shelterin proteins prevent chromosome ends ...The shelterin complex is a macromolecular assembly of proteins that binds to and protects telomeric DNA, which composes the ends of all linear chromosomes. Shelterin proteins prevent chromosome ends from fusing together and from eliciting erroneous induction of DNA damage response pathways. In addition, shelterin proteins play key roles in regulating the recruitment and activation of telomerase, an enzyme that extends telomeric DNA. In fission yeast, Schizosaccharomyces pombe, interactions between the shelterin proteins Ccq1, Tpz1, and Poz1 are important for regulating telomerase-mediated telomere synthesis and thus telomere length homeostasis. Here, we used electron microscopy combined with genetic labeling to define the three-dimensional arrangement of the S. pombe Ccq1-Tpz1-Poz1 (CTP) complex. Crosslinking mass spectrometry was used to identify individual residues that are in proximity to the protein-protein interfaces of the assembled CTP complex. Together, our data provide a first glimpse into the architectural design of the CTP complex and reveals unique interactions that are important in maintaining the S. pombe telomere in a non-extendible state.
DateDeposition: Jul 28, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0462
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0462
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8863.map.gz (map file in CCP4 format, 2371 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
84 pix
3.66 Å/pix.
= 307.44 Å
84 pix
3.66 Å/pix.
= 307.44 Å
84 pix
3.66 Å/pix.
= 307.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.66 Å
Density
Contour Level:0.0462 (by author), 0.0462 (movie #1):
Minimum - Maximum-0.060292363 - 0.10423882
Average (Standard dev.)0.00022372973 (0.009645306)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions848484
Origin0.00.00.0
Limit83.083.083.0
Spacing848484
CellA=B=C: 307.44 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.663.663.66
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z307.440307.440307.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS848484
D min/max/mean-0.0600.1040.000

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Supplemental data

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Sample components

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Entire S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249) as a ...

EntireName: S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249) as a dimer of trimers
Number of components: 1

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Component #1: protein, S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-2...

ProteinName: S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249) as a dimer of trimers
Recombinant expression: No
SourceSpecies: Schizosaccharomyces pombe (fission yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.053 mg/ml / pH: 8
Support film15 mA
VitrificationCryogen name: NONE

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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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
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: 1006
3D reconstructionSoftware: RELION / Resolution: 34.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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