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- EMDB-5818: Negative-stain electron microscopy reconstruction of Tetrahymena ... -

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Basic information

Database: EMDB / ID: 5818
TitleNegative-stain electron microscopy reconstruction of Tetrahymena telomerase (TERT-f, subcomplex lacking Teb1)
Map data3D reconstruction of Tetrahymena telomerase (TERT-f, subcomplex lacking Teb1) using Random Conical Tilt (RCT) method
SampleTelomerase holoenzyme (TERT-f) from Tetrahymena thermophila:
Telomerase holoenzyme
Keywordstelomerase / telomere / Tetrahymena
SourceTetrahymena thermophila (Tetrahymena)
Methodsingle particle reconstruction / negative staining / 35 Å resolution
AuthorsJiang J / Miracco EJ / Hong K / Eckert B / Chan H / Cash DD / Min B / Zhou ZH / Collins K / Feigon J
CitationJournal: Nature / Year: 2013
Title: The architecture of Tetrahymena telomerase holoenzyme.
Authors: Jiansen Jiang / Edward J Miracco / Kyungah Hong / Barbara Eckert / Henry Chan / Darian D Cash / Bosun Min / Z Hong Zhou / Kathleen Collins / Juli Feigon
DateDeposition: Dec 2, 2013 / Header (metadata) release: Jan 15, 2014 / Map release: Jan 15, 2014 / Last update: Jan 15, 2014

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0247
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0247
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_5818.map.gz (map file in CCP4 format, 5005 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
114 pix
4.41 Å/pix.
= 502.74 Å
106 pix
4.41 Å/pix.
= 467.46 Å
106 pix
4.41 Å/pix.
= 467.46 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.41 Å
Contour Level:0.0247 (by author), 0.0247 (movie #1):
Minimum - Maximum-0.04657168 - 0.11971860
Average (Standard dev.)-0.00012710 (0.00509033)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 467.46 Å / B: 467.46 Å / C: 502.74 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.414.414.41
M x/y/z106106114
origin x/y/z0.0000.0000.000
length x/y/z467.460467.460502.740
start NX/NY/NZ-95-75153
MAP C/R/S123
start NC/NR/NS-53-53-57
D min/max/mean-0.0470.120-0.000

Supplemental data

Sample components

Entire Telomerase holoenzyme (TERT-f) from Tetrahymena thermophila

EntireName: Telomerase holoenzyme (TERT-f) from Tetrahymena thermophila
Number of components: 1 / Oligomeric State: Hetero-octamer
MassTheoretical: 500 kDa

Component #1: protein, Telomerase holoenzyme

ProteinName: Telomerase holoenzyme / a.k.a: Telomerase / Oligomeric Details: Hetero-octamer / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 500 kDa
SourceSpecies: Tetrahymena thermophila (Tetrahymena)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: 20 mM HEPES, 50 mM NaCl, 1 mM MgCl2, 1 mM TCEP
pH: 8
Support film200 mesh grid with thin carbon support
Staining0.8% uranyl formate
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: May 4, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 70000 X (nominal), 68027 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3700 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 65 - 65 deg. / Temperature: 298 K
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 315 / Bit depth: 16

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 325 / Details: The RCT 3D reconstruction was done using SPIDER.
3D reconstructionAlgorithm: Random Conical Tilt / Software: SPIDER / CTF correction: Each particle / Resolution: 35 Å / Resolution method: FSC 0.5, semi-independent

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