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

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Basic information

Entry
Database: EMDB / ID: EMD-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)
Sample
  • Complex: 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)
Function / homology
Function and homology information


telomere-telomerase complex assembly / subtelomeric heterochromatin / telomere cap complex / chromosome, telomeric repeat region / meiotic chromosome segregation / meiotic telomere clustering / shelterin complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding ...telomere-telomerase complex assembly / subtelomeric heterochromatin / telomere cap complex / chromosome, telomeric repeat region / meiotic chromosome segregation / meiotic telomere clustering / shelterin complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / telomere organization / molecular adaptor activity / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Adrenocortical dysplasia protein
Similarity search - Domain/homology
Protection of telomeres protein poz1 / Protection of telomeres protein tpz1 / Coiled-coil quantitatively-enriched protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 30.7 Å
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.
History
DepositionJul 28, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 8, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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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

emd_8865.png

Downloads & links

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Map

FileDownload / File: emd_8865.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stain reconstruction of an N-terminally MBP tagged Poz1 in the S. pombe CTP complex (Ccq1 2-716, Tpz1 406-508, Poz1 2-249)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0436 / Movie #1: 0.0436
Minimum - Maximum-0.081371136 - 0.13343428
Average (Standard dev.)-0.0010259209 (±0.010540782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 300.4 Å
α=β=γ: 90.0 °

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)
Components
  • Complex: 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)

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Supramolecule #1: Negative-stain reconstruction of an N-terminally MBP tagged Poz1 ...

SupramoleculeName: 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)
type: complex / ID: 1 / Parent: 0 / Details: Complex is a dimer of trimers
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.064 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMNaH2PO4Sodium phosphate
200.0 mMNaClSodium chloride
5.0 mMC2H6OSBeta mercaptoethanol
StainingType: NEGATIVE / Material: Uranyl acetate
GridPretreatment - Type: GLOW DISCHARGE / Details: 15 mA

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: omega in-column
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 15.6 µm / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 16485
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 1006 / Random conical tilt - Tilt angle: 55 degrees
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 1447
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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