+Open data
-Basic information
Entry | Database: PDB / ID: 7egh | ||||||
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Title | TFIID lobe C subcomplex | ||||||
Components |
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Keywords | TRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation | ||||||
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 I general transcription initiation factor activity ...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 I general transcription initiation factor activity / SLIK (SAGA-like) complex / maintenance of protein location in nucleus / positive regulation of androgen receptor activity / 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 / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor 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 / 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 / regulation of signal transduction by p53 class mediator / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / response to organic cyclic compound / p53 binding / G2/M transition of mitotic cell cycle / protein polyubiquitination / 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 / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / sequence-specific DNA binding / transcription coactivator activity / protein autophosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / transcription by RNA polymerase II / cell differentiation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / positive regulation of apoptotic process / protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
Authors | Chen, X. / Wu, Z. / Li, J. / Zhao, D. / Xu, Y. | ||||||
Citation | Journal: Science / Year: 2021 Title: Structural insights into preinitiation complex assembly on core promoters. Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu / Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7egh.cif.gz | 515.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7egh.ent.gz | 390.6 KB | Display | PDB format |
PDBx/mmJSON format | 7egh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7egh_validation.pdf.gz | 666.9 KB | Display | wwPDB validaton report |
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Full document | 7egh_full_validation.pdf.gz | 674 KB | Display | |
Data in XML | 7egh_validation.xml.gz | 57.8 KB | Display | |
Data in CIF | 7egh_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7egh ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7egh | HTTPS FTP |
-Related structure data
Related structure data | 31117MC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egbC 7egcC 7egdC 7egeC 7egfC 7eggC 7egiC 7egjC 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
-Transcription initiation factor TFIID subunit ... , 5 types, 6 molecules ABFfGH
#1: Protein | Mass: 212956.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Homo sapiens (human) References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase | ||||
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#2: Protein | Mass: 137159.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF2, CIF150, TAF2B / Production host: Homo sapiens (human) / References: UniProt: Q6P1X5 | ||||
#3: Protein | Mass: 72749.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF6, TAF2E, TAFII70 / Production host: Homo sapiens (human) / References: UniProt: P49848 #4: Protein | | Mass: 40325.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, TAF2F, TAFII55 / Production host: Homo sapiens (human) / References: UniProt: Q15545 #5: Protein | | Mass: 34304.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF8, TAFII43, TBN / Production host: Homo sapiens (human) / References: UniProt: Q7Z7C8 |
-DNA chain , 2 types, 2 molecules XY
#6: DNA chain | Mass: 22317.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#7: DNA chain | Mass: 28814.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-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: TFIID lobe C subcomplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 32 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121285 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |