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- EMDB-8865: Negative-stain reconstruction of an N-terminally MBP tagged Poz1 ... -

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Entry
Database: EMDB / ID: 8865
TitleNegative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249)
Map dataNegative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249)
SampleNegative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249):
Function / homologyAdrenocortical dysplasia protein / meiotic spindle pole body / protein binding involved in negative regulation of telomere maintenance via telomerase / telomere-telomerase complex assembly / negative regulation of DNA recombination at telomere / telomeric heterochromatin / meiotic telomere clustering / meiotic chromosome segregation / positive regulation of telomere maintenance / telomere cap complex ...Adrenocortical dysplasia protein / meiotic spindle pole body / protein binding involved in negative regulation of telomere maintenance via telomerase / telomere-telomerase complex assembly / negative regulation of DNA recombination at telomere / telomeric heterochromatin / meiotic telomere clustering / meiotic chromosome segregation / positive regulation of telomere maintenance / 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 / cellular protein localization / telomere organization / negative regulation of telomerase activity / telomere maintenance / positive regulation of telomere maintenance via telomerase / positive regulation of telomerase activity / nuclear chromosome, telomeric region / 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 / 30.7 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: 0.0436
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0436
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8865.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
3 Å/pix.
= 300.4 Å
100 pix
3 Å/pix.
= 300.4 Å
100 pix
3 Å/pix.
= 300.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.004 Å
Density
Contour Level:0.0436 (by author), 0.0436 (movie #1):
Minimum - Maximum-0.081371136 - 0.13343428
Average (Standard dev.)-0.0010259209 (0.010540782)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 300.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.0043.0043.004
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z300.400300.400300.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0810.133-0.001

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Supplemental data

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Sample components

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Entire Negative-stain reconstruction of an N-terminally MBP tagged Poz1 ...

EntireName: Negative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, 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 an N-terminally MBP tag...

ProteinName: Negative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249)
Details: Complex is 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.: 0.064 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: 1447
3D reconstructionSoftware: RELION / Resolution: 30.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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