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

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Basic information

Entry
Database: EMDB / ID: EMD-5135
TitleTBP-lacking S. pombe TFIID
Map dataTBP-lacking S. pombe TFIID
Sample
  • Sample: Native S. pombe TFIID
  • Protein or peptide: TAF1-TAF12
Function / homologyTranscription initiation factor TFIID subunit 12 domain / transcription factor TFIID complex
Function and homology information
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsElmlund H / Baraznenok V / Linder T / Szilagyi Z / Rofougaran R / Hofer A / Hebert H / Lindahl M / Gustafsson CM
CitationJournal: Structure / Year: 2009
Title: Cryo-EM reveals promoter DNA binding and conformational flexibility of the general transcription factor TFIID.
Authors: Hans Elmlund / Vera Baraznenok / Tomas Linder / Zsolt Szilagyi / Reza Rofougaran / Anders Hofer / Hans Hebert / Martin Lindahl / Claes M Gustafsson /
Abstract: The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and ...The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the TFIID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.
History
DepositionOct 19, 2009-
Header (metadata) releaseNov 2, 2009-
Map releaseNov 2, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5135_1.png

Downloads & links

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Map

FileDownload / File: emd_5135.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTBP-lacking S. pombe TFIID
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 100 pix.
= 233. Å		2.33 Å/pix.
x 100 pix.
= 233. Å		2.33 Å/pix.
x 100 pix.
= 233. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.3041123
Minimum - Maximum-4.21842861 - 22.180101390000001
Average (Standard dev.)-0.00138073 (±1.00010693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 233.0 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-4.21822.180-0.001

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Supplemental data

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Sample components

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Entire : Native S. pombe TFIID

EntireName: Native S. pombe TFIID
Components
  • Sample: Native S. pombe TFIID
  • Protein or peptide: TAF1-TAF12

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Supramolecule #1000: Native S. pombe TFIID

SupramoleculeName: Native S. pombe TFIID / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 870 KDa / Theoretical: 870 KDa / Method: GEMMA

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Macromolecule #1: TAF1-TAF12

MacromoleculeName: TAF1-TAF12 / type: protein_or_peptide / ID: 1 / Name.synonym: TFIID / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / synonym: Fission yeast
SequenceGO: transcription factor TFIID complex
InterPro: Transcription initiation factor TFIID subunit 12 domain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: METHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SIMPLE

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