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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31108 | |||||||||
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Title | TFIID-based core PIC on PUMA promoter | |||||||||
![]() | TFIID-based core PIC on PUMA promoter | |||||||||
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Function / homology | ![]() 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 / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / 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 / phosphatase activator activity / SLIK (SAGA-like) complex / RNA polymerase III general transcription initiation factor activity / 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 / hepatocyte differentiation / transcriptional start site selection at RNA polymerase II promoter / 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 - Major Pathway / 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 / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear vitamin D receptor binding / RNA polymerase binding / germinal vesicle / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / Viral Messenger RNA Synthesis / response to L-glutamate / cellular response to ATP / Signaling by FGFR2 IIIa TM / midbrain development / histone acetyltransferase binding / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
![]() | Chen X / Qi Y / Hou H / Wang X / Wu Z / Li J / Xu Y | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 68.2 KB 68.2 KB | Display Display | ![]() |
Images | ![]() | 84 KB | ||
Others | ![]() ![]() ![]() ![]() | 88 MB 7.3 MB 4.5 MB 1.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eg8MC ![]() 7edxC ![]() 7eg7C ![]() 7eg9C ![]() 7egaC ![]() 7egbC ![]() 7egcC ![]() 7egdC ![]() 7egeC ![]() 7egfC ![]() 7eggC ![]() 7eghC ![]() 7egiC ![]() 7egjC 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 | TFIID-based core PIC on PUMA promoter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 7.4 Angstrom TFIID-based core PIC on PUMA promoter with intact DNA
File | emd_31108_additional_1.map | ||||||||||||
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Annotation | 7.4 Angstrom TFIID-based core PIC on PUMA promoter with intact DNA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 7.3 Angstrom TFIID module
File | emd_31108_additional_2.map | ||||||||||||
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Annotation | 7.3 Angstrom TFIID module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.5 Angstrom Pol II module
File | emd_31108_additional_3.map | ||||||||||||
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Annotation | 3.5 Angstrom Pol II module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 5 Angstrom TBP module
File | emd_31108_additional_4.map | ||||||||||||
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Annotation | 5 Angstrom TBP module | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : TFIID-based core PIC on PUMA promoter
+Supramolecule #1: TFIID-based core PIC on PUMA promoter
+Supramolecule #2: TFIID
+Supramolecule #3: RNA POLYMERASE II
+Supramolecule #4: TFIIA
+Supramolecule #5: TFIIB
+Supramolecule #6: TFIIF
+Supramolecule #7: DNA(SCP promoters)
+Macromolecule #1: Transcription initiation factor TFIID subunit 1
+Macromolecule #2: Transcription initiation factor TFIID subunit 2
+Macromolecule #3: Transcription initiation factor TFIID subunit 4
+Macromolecule #4: Transcription initiation factor TFIID subunit 5
+Macromolecule #5: Transcription initiation factor TFIID subunit 6
+Macromolecule #6: Transcription initiation factor TFIID subunit 7
+Macromolecule #7: Transcription initiation factor TFIID subunit 8
+Macromolecule #8: Transcription initiation factor TFIID subunit 9
+Macromolecule #9: Transcription initiation factor TFIID subunit 10
+Macromolecule #10: Transcription initiation factor TFIID subunit 12
+Macromolecule #11: Transcription initiation factor IIA subunit 2
+Macromolecule #12: TATA-box-binding protein
+Macromolecule #13: Transcription initiation factor IIA subunit 1
+Macromolecule #14: Transcription initiation factor IIB
+Macromolecule #15: General transcription factor IIF subunit 1
+Macromolecule #16: General transcription factor IIF subunit 2
+Macromolecule #19: Transcription initiation factor TFIID subunit 3
+Macromolecule #20: Transcription initiation factor TFIID subunit 11
+Macromolecule #21: Transcription initiation factor TFIID subunit 13
+Macromolecule #22: RPB1
+Macromolecule #23: DNA-directed RNA polymerase subunit beta
+Macromolecule #24: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #25: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #26: DNA-directed RNA polymerase II subunit E
+Macromolecule #27: DNA-directed RNA polymerase II subunit F
+Macromolecule #28: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #29: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #30: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #31: RPB10
+Macromolecule #32: RNA_pol_L_2 domain-containing protein
+Macromolecule #33: RPB12
+Macromolecule #17: DNA (85-MER)
+Macromolecule #18: DNA (85-MER)
+Macromolecule #34: ZINC ION
+Macromolecule #35: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7186 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |