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- EMDB-2229: The architecture of human general transcription factor TFIID core... -

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Basic information

Entry
Database: EMDB / ID: EMD-2229
TitleThe architecture of human general transcription factor TFIID core complex
Map dataCryo-EM structure of the recombinant human 3TAF complex
Sample
  • Sample: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 5
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 6
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 9
Keywordshuman TFIID / general transcription factor / transcription / multibac / recombinant protein
Function / homology
Function and homology information


transcription cis-regulatory region binding => GO:0000976 / : / : / transcription factor TFTC complex / transcription factor TFIID complex / viral process / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / actin cytoskeleton / DNA-binding transcription factor activity
Similarity search - Function
: / Transcription initiation factor TAFII31 / TFIID subunit TAF5, NTD2 domain / TAF6, C-terminal HEAT repeat domain / LIS1 homology motif / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.8 Å
AuthorsBieniossek C / Papai G / Schaffitzel C / Garzoni F / Chaillet M / Scheer E / Papadopoulos P / Tora L / Schultz P / Berger I
CitationJournal: Nature / Year: 2013
Title: The architecture of human general transcription factor TFIID core complex.
Authors: Christoph Bieniossek / Gabor Papai / Christiane Schaffitzel / Frederic Garzoni / Maxime Chaillet / Elisabeth Scheer / Petros Papadopoulos / Laszlo Tora / Patrick Schultz / Imre Berger /
Abstract: The initiation of gene transcription by RNA polymerase II is regulated by a plethora of proteins in human cells. The first general transcription factor to bind gene promoters is transcription factor ...The initiation of gene transcription by RNA polymerase II is regulated by a plethora of proteins in human cells. The first general transcription factor to bind gene promoters is transcription factor IID (TFIID). TFIID triggers pre-initiation complex formation, functions as a coactivator by interacting with transcriptional activators and reads epigenetic marks. TFIID is a megadalton-sized multiprotein complex composed of TATA-box-binding protein (TBP) and 13 TBP-associated factors (TAFs). Despite its crucial role, the detailed architecture and assembly mechanism of TFIID remain elusive. Histone fold domains are prevalent in TAFs, and histone-like tetramer and octamer structures have been proposed in TFIID. A functional core-TFIID subcomplex was revealed in Drosophila nuclei, consisting of a subset of TAFs (TAF4, TAF5, TAF6, TAF9 and TAF12). These core subunits are thought to be present in two copies in holo-TFIID, in contrast to TBP and other TAFs that are present in a single copy, conveying a transition from symmetry to asymmetry in the TFIID assembly pathway. Here we present the structure of human core-TFIID determined by cryo-electron microscopy at 11.6 Å resolution. Our structure reveals a two-fold symmetric, interlaced architecture, with pronounced protrusions, that accommodates all conserved structural features of the TAFs including the histone folds. We further demonstrate that binding of one TAF8-TAF10 complex breaks the original symmetry of core-TFIID. We propose that the resulting asymmetric structure serves as a functional scaffold to nucleate holo-TFIID assembly, by accreting one copy each of the remaining TAFs and TBP.
History
DepositionOct 30, 2012-
Header (metadata) releaseNov 7, 2012-
Map releaseJan 9, 2013-
UpdateFeb 13, 2013-
Current statusFeb 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2229-3TA...

Downloads & links

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Map

FileDownload / File: emd_2229.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the recombinant human 3TAF complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 128 pix.
= 260.096 Å		2.03 Å/pix.
x 128 pix.
= 260.096 Å		2.03 Å/pix.
x 128 pix.
= 260.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-8.633073810000001 - 27.51564789
Average (Standard dev.)0.00000002 (±2.00000024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 260.096 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0322.0322.032
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z260.096260.096260.096
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-8.63327.5160.000

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Supplemental data

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Sample components

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Entire : Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.

EntireName: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
Components
  • Sample: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 5
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 6
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 9

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Supramolecule #1000: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.

SupramoleculeName: Recombinant human 3TAF complex containing TAF5, TAF6 and TAF9.
type: sample / ID: 1000 / Details: The sample was fixed by GraFix. / Oligomeric state: Dimer / Number unique components: 3
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: TATA box binding protein (TBP)-associated factor 5

MacromoleculeName: TATA box binding protein (TBP)-associated factor 5 / type: protein_or_peptide / ID: 1 / Name.synonym: TAF5 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 100 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, GO: 0019048
InterPro: WD40 repeat, LIS1 homology motif, TFIID subunit TAF5, NTD2 domain, WD40/YVTN repeat-like-containing domain superfamily, INTERPRO: IPR017986, WD40 repeat, conserved site, G-protein beta WD-40 repeat

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Macromolecule #2: TATA box binding protein (TBP)-associated factor 6

MacromoleculeName: TATA box binding protein (TBP)-associated factor 6 / type: protein_or_peptide / ID: 2 / Name.synonym: TAF6 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 70 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, GO: 0019048
InterPro: TATA box binding protein associated factor (TAF), histone-like fold domain, Histone-fold, TAF6, C-terminal HEAT repeat domain

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Macromolecule #3: TATA box binding protein (TBP)-associated factor 9

MacromoleculeName: TATA box binding protein (TBP)-associated factor 9 / type: protein_or_peptide / ID: 3 / Name.synonym: TAF9 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 32 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: ...GO: actin cytoskeleton, transcription factor TFIID complex, transcription factor TFTC complex, DNA-binding transcription factor activity, transcription cis-regulatory region binding => GO:0000976, GO: 0016573, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process, GO: 0019048
InterPro: Transcription initiation factor TAFII31, Histone-fold

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 50mM HEPES pH 8.0, 150mM KCl
GridDetails: Quantifoil 300 mesh Cu/Rh holey carbon grid R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: 4s, blot force 5

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Electron microscopy

MicroscopeFEI TECNAI 20
DateSep 15, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.16 µm / Number real images: 16 / Average electron dose: 16 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50012 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.45 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsPicking was done with e2boxer from EMAN2, first alignment cycles were done in Imagic and refinement in Spider.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 11987

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