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- EMDB-2231: The architecture of human general transcription factor TFIID core... -

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Basic information

Entry
Database: EMDB / ID: EMD-2231
TitleThe architecture of human general transcription factor TFIID core complex
Map dataCryo-Em structure of the recombinant human 7TAF complex
Sample
  • Sample: Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8, TAF9, TAF10 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
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 8
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 10
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 / modulation by virus of host process / : / protein binding / : / 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 / modulation by virus of host process / : / protein binding / : / transcription factor TFTC complex / transcription factor TFIID complex / viral process / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of DNA-binding transcription factor activity / actin cytoskeleton / transcription coactivator activity / DNA-binding transcription factor activity / protein heterodimerization activity / DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / DNA binding / nucleus
Similarity search - Function
Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 / Bromodomain associated domain / Transcription initiation factor TAFII31 / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / TAF6, C-terminal HEAT repeat domain / : / Transcription initiation factor TFIID, 23-30kDa subunit ...Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 / Bromodomain associated domain / Transcription initiation factor TAFII31 / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / TAF6, C-terminal HEAT repeat domain / : / Transcription initiation factor TFIID, 23-30kDa subunit / 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: 14.3 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
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  • 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-2231-7TA...

Downloads & links

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Map

FileDownload / File: emd_2231.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-Em structure of the recombinant human 7TAF complex
Voxel sizeX=Y=Z: 1.87 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-18.336439129999999 - 42.023067470000001
Average (Standard dev.)-0.00000007 (±1.99999988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.871.871.87
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z299.200299.200299.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-18.33642.023-0.000

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Supplemental data

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Sample components

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Entire : Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8...

EntireName: Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8, TAF9, TAF10 and TAF12.
Components
  • Sample: Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8, TAF9, TAF10 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
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 8
  • Protein or peptide: TATA box binding protein (TBP)-associated factor 10

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Supramolecule #1000: Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8...

SupramoleculeName: Recombinant human 7TAF complex containing TAF4, TAF5, TAF6,, TAF8, TAF9, TAF10 and TAF12.
type: sample / ID: 1000 / Details: The sample was fixed by GraFix. / Oligomeric state: Monomer / Number unique components: 7
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, modulation by virus of host process
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, modulation by virus of host process
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, modulation by virus of host process
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, modulation by virus of host process
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: SAGA complex => GO:0000124, SAGA complex => GO:0000124, transcription factor TFIID complex, transcription factor TFTC complex, DNA binding, transcription coactivator activity, GO: 0043966, positive regulation of DNA-binding transcription factor activity, 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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Macromolecule #6: TATA box binding protein (TBP)-associated factor 8

MacromoleculeName: TATA box binding protein (TBP)-associated factor 8 / type: protein_or_peptide / ID: 6 / Name.synonym: TAF8 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 43 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: protein heterodimerization activity, protein binding, transcription factor TFIID complex, perinuclear region of cytoplasm, nucleus, nucleolus, DNA-templated transcription
InterPro: Bromodomain associated domain, Histone-fold, Transcription factor TFIID, subunit 8, C-terminal

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Macromolecule #7: TATA box binding protein (TBP)-associated factor 10

MacromoleculeName: TATA box binding protein (TBP)-associated factor 10 / type: protein_or_peptide / ID: 7 / Name.synonym: TAF10 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Molecular weightTheoretical: 43 KDa
Recombinant expressionOrganism: Baculovirus EMBacY / Recombinant plasmid: pTF
SequenceGO: protein heterodimerization activity, protein binding, transcription factor TFIID complex, perinuclear region of cytoplasm, nucleus, nucleolus, DNA-templated transcription
InterPro: Transcription initiation factor TFIID, 23-30kDa subunit

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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 POLARA 300
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 78120 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: OTHER
DateJun 18, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 14.5 µm / Number real images: 170 / Average electron dose: 16 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic, Spider / Number images used: 44663
DetailsPicking was done with e2boxer from EMAN2, first alignment cycles were done in Imagic and refinement in Spider.

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