+Open data
-Basic information
Entry | Database: PDB / ID: 5fur | ||||||
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Title | Structure of human TFIID-IIA bound to core promoter DNA | ||||||
Components |
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Keywords | TRANSCRIPTION / TFIID / TFIIA / RNA POLYMERASE II / GENERAL TRANSCRIPTION FACTORS / PREINITIATION COMPLEX / CORE PROMOTER / DNA BINDING | ||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / 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 transcription factor SL1 complex ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / DNA-templated transcription open complex formation / TFIIH-class transcription factor complex binding / 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 transcription factor SL1 complex / RNA polymerase I general transcription initiation factor 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 / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of androgen receptor activity / 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 / 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 / cellular response to ATP / midbrain development / histone acetyltransferase binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / estrogen receptor signaling pathway / male germ cell nucleus / negative regulation of ubiquitin-dependent protein catabolic process / regulation of DNA repair / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / histone acetyltransferase / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / euchromatin / response to organic cyclic compound / p53 binding / G2/M transition of mitotic cell cycle / protein polyubiquitination / cell junction / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein binding / kinase activity / peptidyl-serine phosphorylation / DNA-binding transcription factor binding / ubiquitin-dependent protein catabolic process / spermatogenesis / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / protein autophosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å | ||||||
Authors | Louder, R.K. / He, Y. / Lopez-Blanco, J.R. / Fang, J. / Chacon, P. / Nogales, E. | ||||||
Citation | Journal: 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 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A **-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5fur.cif.gz | 545.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fur.ent.gz | 397 KB | Display | PDB format |
PDBx/mmJSON format | 5fur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fur_validation.pdf.gz | 789 KB | Display | wwPDB validaton report |
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Full document | 5fur_full_validation.pdf.gz | 994.8 KB | Display | |
Data in XML | 5fur_validation.xml.gz | 98.4 KB | Display | |
Data in CIF | 5fur_validation.cif.gz | 145.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fur ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fur | HTTPS FTP |
-Related structure data
Related structure data | 3305MC 3304C 3306C 3307C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37729.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P20226 |
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-TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT ... , 3 types, 3 molecules BCD
#2: Protein/peptide | Mass: 5098.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52655 |
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#3: Protein/peptide | Mass: 5594.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52655 |
#4: Protein | Mass: 11275.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P52657 |
-DNA chain , 2 types, 2 molecules EF
#5: DNA chain | Mass: 27664.635 Da / Num. of mol.: 1 / Fragment: NONTEMPLATE STRAND / Source method: isolated from a natural source Details: A COMPOSITE SEQUENCE COMBINING SEVERAL PROMOTER MOTIFS FROM HUMANS A Source: (natural) HOMO SAPIENS (human) / Cell line: HELA |
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#6: DNA chain | Mass: 28485.129 Da / Num. of mol.: 1 / Fragment: TEMPLATE STRAND / Source method: isolated from a natural source Details: A COMPOSITE SEQUENCE COMBINING SEVERAL PROMOTER MOTIFS FROM HUMANS A Source: (natural) HOMO SAPIENS (human) / Cell line: HELA |
-TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT ... , 5 types, 6 molecules GHIJKL
#7: Protein | Mass: 215152.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase | ||
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#8: Protein | Mass: 40325.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q15545 | ||
#9: Protein | Mass: 137159.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q6P1X5 | ||
#10: Protein | Mass: 72749.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: P49848 #11: Protein | | Mass: 34304.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HELA / References: UniProt: Q7Z7C8 |
-Details
Sequence details | THE SUPER CORE PROMOTER SEQUENCE IS DESCRIBED IN JUVEN- GERSHON. ET AL. (2006) NATURE METHODS, 3, P.917-922. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: HUMAN TFIID-TFIIA COMPLEX BOUND TO SUPER CORE PROMOTER DNA Type: COMPLEX |
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Buffer solution | Name: 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40 pH: 7.9 Details: 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN / Date: Aug 11, 2014 Details: THE CAMERA WAS OPERATED IN COUNTING MODE WITH A DOSE RATE OF 8 ELECTRONS PER PIXEL PER SECOND, WITH A TOTAL EXPOSURE TIME OF 10 SECONDS FRACTIONATED OVER 20 FRAMES. |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 37879 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 1253 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 8.5 Å / Num. of particles: 22050 / Actual pixel size: 1.32 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3305. (DEPOSITION ID: 14001). Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||
Refinement | Highest resolution: 8.5 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.5 Å
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