+Open data
-Basic information
Entry | Database: PDB / ID: 7egb | |||||||||
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Title | TFIID-based holo PIC on SCP promoter | |||||||||
Components |
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Keywords | TRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation | |||||||||
Function / homology | Function and homology information microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex ...microfibril binding / spermine transport / negative regulation of MHC class I biosynthetic process / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / TFIIH-class transcription factor complex binding / nucleotide-excision repair, DNA duplex unwinding / negative regulation of protein autoubiquitination / central nervous system myelin formation / positive regulation of mitotic recombination / transcription factor TFTC complex / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / SLIK (SAGA-like) complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / 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 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / positive regulation of response to cytokine stimulus / DNA 5'-3' helicase / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / DNA 3'-5' helicase / RNA polymerase binding / box C/D snoRNP assembly / [RNA-polymerase]-subunit kinase Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Chen, X. / Wu, Z. / Hou, H. / Qi, Y. / Wang, X. / Li, J. / Xu, Y. | |||||||||
Funding support | 1items
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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 | 7egb.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7egb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7egb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7egb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7egb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7egb_validation.xml.gz | 292.1 KB | Display | |
Data in CIF | 7egb_validation.cif.gz | 478.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7egb ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7egb | HTTPS FTP |
-Related structure data
Related structure data | 31111MC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egcC 7egdC 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
-Protein , 8 types, 8 molecules 089PUxyz
#1: Protein | Mass: 35873.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Homo sapiens (human) / References: UniProt: P51948 |
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#9: Protein | Mass: 39090.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / Production host: Homo sapiens (human) References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
#10: Protein | Mass: 37695.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNH / Production host: Homo sapiens (human) / References: UniProt: P51946 |
#22: 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 |
#27: Protein | Mass: 49516.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Homo sapiens (human) / References: UniProt: P29083 |
#43: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
#44: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25 |
#45: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TRS6 |
-General transcription factor IIH subunit ... , 5 types, 5 molecules 12345
#2: Protein | Mass: 62116.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Homo sapiens (human) / References: UniProt: P32780 |
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#3: Protein | Mass: 44481.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Homo sapiens (human) / References: UniProt: Q13888 |
#4: Protein | Mass: 34416.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Homo sapiens (human) / References: UniProt: Q13889 |
#5: Protein | Mass: 52245.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Homo sapiens (human) / References: UniProt: Q92759 |
#6: Protein | Mass: 8060.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Homo sapiens (human) / References: UniProt: Q6ZYL4 |
-General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 67
#7: Protein | Mass: 89404.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Homo sapiens (human) / References: UniProt: P19447, DNA helicase |
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#8: Protein | Mass: 87021.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Homo sapiens (human) / References: UniProt: P18074, DNA helicase |
-Transcription initiation factor ... , 17 types, 23 molecules ABDdEeFfGHIiJjLlOQRVckm
#11: 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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#12: 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 | ||||||||||||||||||||||||||||
#13: 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 #14: 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 #15: 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 #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #21: 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 #23: 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 #24: Protein | | Mass: 34877.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Homo sapiens (human) / References: UniProt: Q00403, histone acetyltransferase #28: Protein | | Mass: 33106.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E2, TF2E2 / Production host: Homo sapiens (human) / References: UniProt: P29084 #31: 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 #32: 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 #33: 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 |
-General transcription factor IIF subunit ... , 2 types, 2 molecules ST
#25: Protein | Mass: 58343.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2F1, RAP74 / Production host: Homo sapiens (human) / References: UniProt: P35269 |
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#26: Protein | Mass: 28427.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2F2, RAP30 / Production host: Homo sapiens (human) / References: UniProt: P13984, DNA helicase |
-DNA chain , 2 types, 2 molecules XY
#29: DNA chain | Mass: 29188.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#30: DNA chain | Mass: 21094.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-DNA-directed RNA ... , 9 types, 9 molecules opqrstuvw
#34: Protein | Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase |
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#35: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: A0A4X1TVZ5, DNA-directed RNA polymerase |
#36: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3 |
#37: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481BYI6 |
#38: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VTX4 |
#39: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VEK9 |
#40: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7 |
#41: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULF2 |
#42: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899 |
-Non-polymers , 3 types, 19 molecules
#46: Chemical | ChemComp-ZN / #47: Chemical | ChemComp-SF4 / | #48: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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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 |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | 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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92806 / Symmetry type: POINT |