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- EMDB-3305: Structure of human TFIID-IIA bound to core promoter DNA (locally-... -

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Basic information

Entry
Database: EMDB / ID: EMD-3305
TitleStructure of human TFIID-IIA bound to core promoter DNA (locally-refined BC core)
Map dataLocally-refined BC-core of human TFIID-IIA bound to super core promoter DNA
Sample
  • Sample: Human TFIID-TFIIA complex bound to super core promoter DNA
  • Protein or peptide: General transcription factor IID
  • Protein or peptide: General transcription factor IIA
  • DNA: Super core promoter
KeywordsTFIID / TFIIA / transcription / RNA polymerase II / general transcription factors / preinitiation complex / core promoter / DNA binding
Function / homology
Function and homology information


negative regulation of MHC class I biosynthetic process / spermine transport / DNA-templated transcription open complex formation / positive regulation of androgen receptor signaling pathway / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / negative regulation of MHC class II biosynthetic process / transcription factor TFTC complex / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition ...negative regulation of MHC class I biosynthetic process / spermine transport / DNA-templated transcription open complex formation / positive regulation of androgen receptor signaling pathway / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / negative regulation of MHC class II biosynthetic process / transcription factor TFTC complex / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / histone H4K16ac reader activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / maintenance of protein location in nucleus / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / nuclear vitamin D receptor binding / regulation of fat cell differentiation / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / histone acetyltransferase binding / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / midbrain development / cellular response to ATP / negative regulation of signal transduction by p53 class mediator / negative regulation of cell cycle / aryl hydrocarbon receptor binding / ubiquitin conjugating enzyme activity / transcription initiation at RNA polymerase I promoter / TFIIB-class transcription factor binding / P-TEFb complex binding / RNA Polymerase I Transcription Initiation / MLL1 complex / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase activity / core promoter sequence-specific DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / negative regulation of protein kinase activity / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / estrogen receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / nuclear receptor binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / euchromatin / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M transition of mitotic cell cycle / protein polyubiquitination / kinase activity / p53 binding / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein autophosphorylation / chromatin organization / ubiquitin-dependent protein catabolic process / spermatogenesis / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / non-specific serine/threonine protein kinase
Similarity search - Function
TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAF2 Ig-like domain / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain transcription factors and PHD domain containing proteins ...TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAF2 Ig-like domain / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated / Bromodomain associated domain / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Aminopeptidase N-like , N-terminal domain superfamliy / TBP domain superfamily / Peptidase M4/M1, CTD superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsLouder RK / He Y / Lopez-Blanco JR / Fang J / Chacon P / Nogales E
CitationJournal: Nature / Year: 2016
Title: Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.
Authors: Robert K Louder / Yuan He / José Ramón López-Blanco / Jie Fang / Pablo Chacón / Eva Nogales /
Abstract: The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the ...The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.
History
DepositionJan 27, 2016-
Header (metadata) releaseFeb 3, 2016-
Map releaseMar 30, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-5fur
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fur
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Structure viewerEM map:
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Supplemental images

emd_3305.png

Downloads & links

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Map

FileDownload / File: emd_3305.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally-refined BC-core of human TFIID-IIA bound to super core promoter DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 384 pix.
= 506.88 Å		1.32 Å/pix.
x 384 pix.
= 506.88 Å		1.32 Å/pix.
x 384 pix.
= 506.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.02489047 - 0.04919277
Average (Standard dev.)0.00008145 (±0.00130076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 506.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z506.880506.880506.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0250.0490.000

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Supplemental data

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Sample components

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Entire : Human TFIID-TFIIA complex bound to super core promoter DNA

EntireName: Human TFIID-TFIIA complex bound to super core promoter DNA
Components
  • Sample: Human TFIID-TFIIA complex bound to super core promoter DNA
  • Protein or peptide: General transcription factor IID
  • Protein or peptide: General transcription factor IIA
  • DNA: Super core promoter

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Supramolecule #1000: Human TFIID-TFIIA complex bound to super core promoter DNA

SupramoleculeName: Human TFIID-TFIIA complex bound to super core promoter DNA
type: sample / ID: 1000 / Number unique components: 3
Molecular weightTheoretical: 1.34 MDa

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Macromolecule #1: General transcription factor IID

MacromoleculeName: General transcription factor IID / type: protein_or_peptide / ID: 1 / Name.synonym: TFIID / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa / synonym: Human / Organelle: Nucleus / Location in cell: Nuclear extract
Molecular weightTheoretical: 1.26 MDa

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Macromolecule #2: General transcription factor IIA

MacromoleculeName: General transcription factor IIA / type: protein_or_peptide / ID: 2 / Name.synonym: TFIIA / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 27 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: Super core promoter

MacromoleculeName: Super core promoter / type: dna / ID: 3 / Name.synonym: SCP
Details: The super core promoter is a composite sequence combining promoter motifs from several strong promoters from humans and D. melanogaster.
Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56 KDa
SequenceString:
GAAGGGCGCC TATAAAAGGG GGTGGGGGCG CGTTCGTCCT CAGTCGCGAT CGAACACTCG AGCCGAGCAG ACGTGCCTAC GGACCATGG

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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

Concentration0.05 mg/mL
BufferpH: 7.9
Details: 10 mM HEPES, 10 mM MgCl2, 50 mM KCl, 3% trehalose 1 mM DTT, 0.0125% NP-40
GridDetails: Amorphous continuous carbon over C-flat holey carbon support (4 um holes with 2 um spacing) on 400 mesh copper grid.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: Incubate 4 ul of sample on grid for 10 minutes, then blot for 4 seconds with force 15.

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Electron microscopy

MicroscopeFEI TITAN
DetailsThe camera was operated in counting mode with a dose rate of 8 electrons/pixel per second, with a total exposure time of 10 seconds fractionated over 20 frames.
DateAug 11, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1253 / Average electron dose: 46 e/Å2
Details: Whole-micrograph drift correction was performed using MotionCorr before averaging the frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37879 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsFinal rounds of 3D image classification and refinement were performed within a mask around the promoter-bound BC-core of TFIID, comprising lobes A2, B, and C.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: OTHER / Software - Name: CTFFIND4, RELION, Bsoft
Details: After whole micrograph drift correction, per-particle beam-induced motion and radiation damage were corrected using the particle polishing procedure within RELION. Final map was filtered ...Details: After whole micrograph drift correction, per-particle beam-induced motion and radiation damage were corrected using the particle polishing procedure within RELION. Final map was filtered according to local resolution using Bsoft.
Number images used: 22050
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1nvp

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5fur:
Structure of human TFIID-IIA bound to core promoter DNA

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Atomic model buiding 2

Initial modelPDB ID:

4rgw

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5fur:
Structure of human TFIID-IIA bound to core promoter DNA

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Atomic model buiding 3

Initial modelPDB ID:

4atg

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5fur:
Structure of human TFIID-IIA bound to core promoter DNA

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