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- EMDB-5135: TBP-lacking S. pombe TFIID -

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Basic information

Database: EMDB / ID: 5135
TitleTBP-lacking S. pombe TFIID
SampleNative S. pombe TFIID
SourceSchizosaccharomyces pombe / yeast / Fission yeast / シゾサッカロミセス・ポンベ /
Map dataTBP-lacking S. pombe TFIID
Methodsingle particle reconstruction, at 10 Å resolution
AuthorsElmlund H / Baraznenok V / Linder T / Szilagyi Z / Rofougaran R / Hofer A / Hebert H / Lindahl M / Gustafsson CM
CitationStructure, 2009, 17, 1442-1452

Structure, 2009, 17, 1442-1452 Yorodumi Papers
Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID.
Hans Elmlund / Vera Baraznenok / Tomas Linder / Zsolt Szilagyi / Reza Rofougaran / Anders Hofer / Hans Hebert / Martin Lindahl / Claes M Gustafsson

DateDeposition: Oct 19, 2009 / Header (metadata) release: Nov 2, 2009 / Map release: Nov 2, 2009 / Last update: Oct 24, 2012

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.304112345
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.304112345
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5135.map.gz (map file in CCP4 format, 3908 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.33 Å/pix.
= 233. Å
100 pix
2.33 Å/pix.
= 233. Å
100 pix
2.33 Å/pix.
= 233. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.33 Å
Contour Level:0.2 (by author), 0.3041123 (movie #1):
Minimum - Maximum-4.21842861 - 22.18010139
Average (Standard dev.)-0.00138073 (1.00010693)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 233 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z233.000233.000233.000
start NX/NY/NZ-34-26-72
MAP C/R/S123
start NC/NR/NS-50-50-50
D min/max/mean-4.21822.180-0.001

Supplemental data

Sample components

Entire Native S. pombe TFIID

EntireName: Native S. pombe TFIID / Number of components: 1
MassTheoretical: 870 kDa / Experimental: 870 kDa / Measured by: GEMMA

Component #1: protein, TAF1-TAF12

ProteinName: TAF1-TAF12 / a.k.a: TFIID / Recombinant expression: No
SourceSpecies: Schizosaccharomyces pombe / yeast / Fission yeast / シゾサッカロミセス・ポンベ /
External referencesInterPro: InterPro: 003228 / Gene Ontology: GO: 0005669

Experimental details

Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: METHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Side entry / Model: GATAN LIQUID NITROGEN

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: RAD, cross-common lines / Software: SIMPLE / Resolution: 10 Å / Resolution method: FSC 0.5

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