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- EMDB-2230: The architecture of human general transcription factor TFIID core... -

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Basic information

Entry
Database: EMDB / ID: EMD-2230
TitleThe architecture of human general transcription factor TFIID core complex
Map dataCryo-EM structure of the recombinant human core-TFIID subcomplex
Sample
  • Sample: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12.
  • 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
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 4
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 12
Keywordshuman TFIID / general transcription factor / transcription / multibac / recombinant protein
Function / homology
Function and homology information


SAGA complex => GO:0000124 / SAGA complex => GO:0000124 / : / transcription cis-regulatory region binding => GO:0000976 / : / : / transcription factor TFTC complex / transcription factor TFIID complex / viral process / : ...SAGA complex => GO:0000124 / SAGA complex => GO:0000124 / : / 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 / transcription coactivator activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 / Transcription initiation factor TAFII31 / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / LIS1 homology motif / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold ...: / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 / Transcription initiation factor TAFII31 / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 12 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: 11.6 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: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2230-cor...

Downloads & links

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Map

FileDownload / File: emd_2230.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the recombinant human core-TFIID subcomplex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.05 Å/pix.
x 133 pix.
= 405.384 Å		3.05 Å/pix.
x 133 pix.
= 405.384 Å		3.05 Å/pix.
x 133 pix.
= 405.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-12.97180176 - 40.505496979999997
Average (Standard dev.)0.00018952 (±0.99185783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-66-66-66
Dimensions133133133
Spacing133133133
CellA=B=C: 405.384 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.0483.0483.048
M x/y/z133133133
origin x/y/z0.0000.0000.000
length x/y/z405.384405.384405.384
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-66-66-66
NC/NR/NS133133133
D min/max/mean-12.97240.5050.000

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Supplemental data

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Sample components

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Entire : Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6,...

EntireName: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12.
Components
  • Sample: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12.
  • 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
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 4
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 12

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Supramolecule #1000: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6,...

SupramoleculeName: Recombinant human core-TFIID complex containing TAF4, TAF5, TAF6, TAF9 and TAF12.
type: sample / ID: 1000 / Details: The sample was fixed by GraFix. / Oligomeric state: Dimer / Number unique components: 5
Molecular weightTheoretical: 700 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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Macromolecule #4: TATA box binding protein (TBP)-associated factor 4

MacromoleculeName: TATA box binding protein (TBP)-associated factor 4 / type: protein_or_peptide / ID: 4 / Name.synonym: TAF4 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 135 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: TAFH/NHR1, Transcription initiation factor TFIID component TAF4, C-terminal, Histone-fold

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Macromolecule #5: TATA box binding protein (TBP)-associated factor 12

MacromoleculeName: TATA box binding protein (TBP)-associated factor 12 / type: protein_or_peptide / ID: 5 / Name.synonym: TAF12 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 15 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: SAGA complex => GO:0000124, SAGA complex => GO:0000124, transcription factor TFIID complex, transcription factor TFTC complex, DNA binding, transcription coactivator activity, GO: 0043966, GO: ...GO: SAGA complex => GO:0000124, SAGA complex => GO:0000124, transcription factor TFIID complex, transcription factor TFTC complex, DNA binding, transcription coactivator activity, GO: 0043966, GO: 0051091, transcription elongation by RNA polymerase II, transcription initiation at RNA polymerase II promoter, viral process
InterPro: Histone-fold, 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

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
DateMay 7, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15.24 µm / Number real images: 23 / 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: 3.749 µm / Nominal defocus min: 1.851 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: 11.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 12566

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Atomic model buiding 1

Initial modelPDB ID:

1taf


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

1h3o


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 3

Initial modelPDB ID:

2pbi


Chain - Chain ID: D
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 4

Initial modelPDB ID:

2j49


Chain - Chain ID: A
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 5

Initial modelPDB ID:

2p6v


Chain - Chain ID: A
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 6

Initial modelPDB ID:

4atg


Chain - Chain ID: A
SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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