+Open data
-Basic information
Entry | Database: PDB / ID: 7egd | ||||||
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Title | SCP promoter-bound TFIID-TFIIA in initial TBP-loading state | ||||||
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 / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex ...spermine transport / negative regulation of MHC class I biosynthetic process / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase transcription factor SL1 complex / 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 I core promoter sequence-specific DNA binding / hepatocyte differentiation / 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 response to cytokine stimulus / 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 / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / positive regulation by host of viral transcription / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / nuclear vitamin D receptor binding / RNA polymerase binding / box C/D snoRNP assembly / limb development / regulation of fat cell differentiation / RNA Polymerase I Transcription Termination / transcription preinitiation complex / SAGA complex / nuclear thyroid hormone receptor binding / inner cell mass cell proliferation / midbrain development / response to L-glutamate / cellular response to ATP / histone acetyltransferase binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / regulation of RNA splicing / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / transcription initiation at RNA polymerase I promoter / MLL1 complex / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / negative regulation of cell cycle / P-TEFb complex binding / embryonic placenta development / somitogenesis / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of intrinsic apoptotic signaling pathway / regulation of DNA repair / core promoter sequence-specific DNA binding / histone acetyltransferase activity / ovarian follicle development / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / estrogen receptor signaling pathway / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / male germ cell nucleus / DNA-templated transcription initiation / nuclear receptor binding / nuclear estrogen receptor binding / promoter-specific chromatin binding / peptidyl-threonine phosphorylation / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lysine-acetylated histone binding / negative regulation of protein kinase activity / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / euchromatin Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.75 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 | 7egd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7egd.ent.gz | 886.1 KB | Display | PDB format |
PDBx/mmJSON format | 7egd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7egd_validation.pdf.gz | 895.9 KB | Display | wwPDB validaton report |
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Full document | 7egd_full_validation.pdf.gz | 911 KB | Display | |
Data in XML | 7egd_validation.xml.gz | 123.2 KB | Display | |
Data in CIF | 7egd_validation.cif.gz | 198.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7egd ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7egd | HTTPS FTP |
-Related structure data
Related structure data | 31113MC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egbC 7egcC 7egeC 7egfC 7eggC 7eghC 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 ... , 13 types, 19 molecules ABDdEeFfGHIiJjLlckm
#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: 110221.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135 / Production host: Homo sapiens (human) / References: UniProt: O00268 #4: Protein | Mass: 86932.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF5, TAF2D / Production host: Homo sapiens (human) / References: UniProt: Q15542 #5: 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 #6: 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 #7: 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 #8: Protein | Mass: 29006.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF9, TAF2G, TAFII31 / Production host: Homo sapiens (human) / References: UniProt: Q16594 #9: Protein | Mass: 21731.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF10, TAF2A, TAF2H, TAFII30 / Production host: Homo sapiens (human) / References: UniProt: Q12962 #10: Protein | Mass: 17948.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF12, TAF15, TAF2J, TAFII20 / Production host: Homo sapiens (human) / References: UniProt: Q16514 #16: Protein | | Mass: 103769.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF3 / Production host: Homo sapiens (human) / References: UniProt: Q5VWG9 #17: Protein | | Mass: 23340.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF11, TAF2I, PRO2134 / Production host: Homo sapiens (human) / References: UniProt: Q15544 #18: Protein | | Mass: 14307.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TAF13, TAF2K, TAFII18 / Production host: Homo sapiens (human) / References: UniProt: Q15543 |
-Transcription initiation factor IIA subunit ... , 2 types, 2 molecules OQ
#11: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Homo sapiens (human) / References: UniProt: P52657 |
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#13: Protein | Mass: 41544.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Homo sapiens (human) / References: UniProt: P52655 |
-Protein , 1 types, 1 molecules P
#12: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Homo sapiens (human) / References: UniProt: P20226 |
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-DNA chain , 2 types, 2 molecules XY
#14: 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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#15: DNA chain | Mass: 22090.072 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: SCP promoter-bound TFIID-TFIIA in initial TBP-loading state 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 / Grid type: Quantifoil R1.2/1.3 |
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 |
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: 6.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100170 / Symmetry type: POINT |