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- EMDB-3305: Structure of human TFIID-IIA bound to core promoter DNA (locally-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3305 | |||||||||
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Title | Structure of human TFIID-IIA bound to core promoter DNA (locally-refined BC core) | |||||||||
![]() | Locally-refined BC-core of human TFIID-IIA bound to super core promoter DNA | |||||||||
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![]() | TFIID / TFIIA / transcription / RNA polymerase II / general transcription factors / preinitiation complex / core promoter / DNA binding | |||||||||
Function / homology | ![]() spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity ...spermine transport / negative regulation of MHC class I biosynthetic process / DNA-templated transcription open complex formation / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / TFIIH-class transcription factor complex 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 / positive regulation of androgen receptor activity / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / transcription regulator inhibitor activity / nuclear vitamin D receptor binding / RNA polymerase II general transcription initiation factor binding / SAGA complex / regulation of fat cell differentiation / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / inner cell mass cell proliferation / cellular response to ATP / midbrain development / 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 / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / MLL1 complex / transcription factor TFIID complex / TFIIB-class transcription factor binding / negative regulation of cell cycle / P-TEFb complex binding / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / estrogen receptor signaling pathway / regulation of DNA repair / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / nuclear receptor binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / euchromatin / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / response to organic cyclic compound / protein polyubiquitination / G2/M transition of mitotic cell cycle / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / cell junction / kinase activity / ubiquitin-dependent protein catabolic process / spermatogenesis / peptidyl-serine phosphorylation / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / protein autophosphorylation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
![]() | Louder RK / He Y / Lopez-Blanco JR / Fang J / Chacon P / Nogales E | |||||||||
![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16 KB | Display | ![]() |
Images | ![]() | 63.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 223.5 KB | Display | ![]() |
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Full document | ![]() | 222.6 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5furMC ![]() 3304C ![]() 3306C ![]() 3307C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Locally-refined BC-core of human TFIID-IIA bound to super core promoter DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human TFIID-TFIIA complex bound to super core promoter DNA
Entire | Name: Human TFIID-TFIIA complex bound to super core promoter DNA |
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Components |
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-Supramolecule #1000: Human TFIID-TFIIA complex bound to super core promoter DNA
Supramolecule | Name: Human TFIID-TFIIA complex bound to super core promoter DNA type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 1.34 MDa |
-Macromolecule #1: General transcription factor IID
Macromolecule | Name: General transcription factor IID / type: protein_or_peptide / ID: 1 / Name.synonym: TFIID / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.26 MDa |
-Macromolecule #2: General transcription factor IIA
Macromolecule | Name: General transcription factor IIA / type: protein_or_peptide / ID: 2 / Name.synonym: TFIIA / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #3: Super core promoter
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56 KDa |
Sequence | String: GAAGGGCGCC TATAAAAGGG GGTGGGGGCG CGTTCGTCCT CAGTCGCGAT CGAACACTCG AGCCGAGCAG ACGTGCCTAC GGACCATGG |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.9 Details: 10 mM HEPES, 10 mM MgCl2, 50 mM KCl, 3% trehalose 1 mM DTT, 0.0125% NP-40 |
Grid | Details: Amorphous continuous carbon over C-flat holey carbon support (4 um holes with 2 um spacing) on 400 mesh copper grid. |
Vitrification | Cryogen 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
Microscope | FEI TITAN |
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Details | The 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. |
Date | Aug 11, 2014 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated 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 stage | Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5fur: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5fur: |