+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31112 | |||||||||
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Title | p53-bound TFIID-based holo PIC on HDM2 promoter | |||||||||
Map data | p53-bound TFIID-based holo PIC on HDM2 promoter | |||||||||
Sample |
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Keywords | TFIID / preinitiation complex / core promoter / transcription initiation / TRANSCRIPTION | |||||||||
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 / nucleotide-excision repair, DNA duplex unwinding / TFIIH-class transcription factor complex binding / negative regulation of protein autoubiquitination / central nervous system myelin formation / positive regulation of core promoter binding / transcription factor TFTC complex / RNA polymerase II core complex assembly / positive regulation of mitotic recombination / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / RNA polymerase transcription factor SL1 complex / ventricular system development / snRNA transcription by RNA polymerase II / hair cell differentiation / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly / SLIK (SAGA-like) complex / 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 / 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 / TFIIF-class transcription factor complex binding / hepatocyte differentiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcriptional start site selection at RNA polymerase II 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 / positive regulation of response to cytokine stimulus / transcription factor TFIIF complex / DNA 5'-3' helicase / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / adult heart development / positive regulation of androgen receptor activity / transcription factor TFIIA complex / female germ cell nucleus / G protein-coupled receptor internalization / C2H2 zinc finger domain binding / male pronucleus / female pronucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / transcription regulator inhibitor activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / RNA polymerase binding / box C/D snoRNP assembly / [RNA-polymerase]-subunit kinase / DNA 3'-5' helicase Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Chen X / Wu Z | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31112.map.gz | 285 MB | EMDB map data format | |
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Header (meta data) | emd-31112-v30.xml emd-31112.xml | 93.7 KB 93.7 KB | Display Display | EMDB header |
Images | emd_31112.png | 47.8 KB | ||
Filedesc metadata | emd-31112.cif.gz | 20.9 KB | ||
Others | emd_31112_additional_1.map.gz emd_31112_additional_2.map.gz emd_31112_additional_3.map.gz emd_31112_additional_4.map.gz emd_31112_additional_5.map.gz emd_31112_additional_6.map.gz | 4.8 MB 262.9 MB 262 MB 15.5 MB 5.4 MB 21.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31112 | HTTPS FTP |
-Validation report
Summary document | emd_31112_validation.pdf.gz | 403.7 KB | Display | EMDB validaton report |
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Full document | emd_31112_full_validation.pdf.gz | 403.3 KB | Display | |
Data in XML | emd_31112_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_31112_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31112 | HTTPS FTP |
-Related structure data
Related structure data | 7egcMC 7edxC 7eg7C 7eg8C 7eg9C 7egaC 7egbC 7egdC 7egeC 7egfC 7eggC 7eghC 7egiC 7egjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31112.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | p53-bound TFIID-based holo PIC on HDM2 promoter | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: 2.9 Angstrom Pol II module
File | emd_31112_additional_1.map | ||||||||||||
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Annotation | 2.9 Angstrom Pol II module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.5 Angstrom TBP module
File | emd_31112_additional_2.map | ||||||||||||
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Annotation | 3.5 Angstrom TBP module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3.5 Angstrom CAK module
File | emd_31112_additional_3.map | ||||||||||||
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Annotation | 3.5 Angstrom CAK module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 4.7 Angstrom TFIIH module
File | emd_31112_additional_4.map | ||||||||||||
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Annotation | 4.7 Angstrom TFIIH module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 4.5 Angstrom TFIID module
File | emd_31112_additional_5.map | ||||||||||||
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Annotation | 4.5 Angstrom TFIID module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 4.3 Angstrom TFIIE module
File | emd_31112_additional_6.map | ||||||||||||
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Annotation | 4.3 Angstrom TFIIE module | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : p53-bound TFIID-based holo PIC on HDM2 promoter
+Supramolecule #1: p53-bound TFIID-based holo PIC on HDM2 promoter
+Supramolecule #2: TFIID
+Supramolecule #3: RNA POLYMERASE II
+Supramolecule #4: TFIIA
+Supramolecule #5: TFIIB
+Supramolecule #6: TFIIF
+Supramolecule #7: DNA(HDM2 promoters)
+Supramolecule #8: TFIIH
+Macromolecule #1: CDK-activating kinase assembly factor MAT1
+Macromolecule #2: General transcription factor IIH subunit 1
+Macromolecule #3: General transcription factor IIH subunit 2
+Macromolecule #4: General transcription factor IIH subunit 3
+Macromolecule #5: General transcription factor IIH subunit 4
+Macromolecule #6: General transcription factor IIH subunit 5
+Macromolecule #7: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #9: Cyclin-dependent kinase 7
+Macromolecule #10: Cyclin-H
+Macromolecule #11: Transcription initiation factor TFIID subunit 1
+Macromolecule #12: Transcription initiation factor TFIID subunit 2
+Macromolecule #13: Transcription initiation factor TFIID subunit 4
+Macromolecule #14: Transcription initiation factor TFIID subunit 5
+Macromolecule #15: Transcription initiation factor TFIID subunit 6
+Macromolecule #16: Transcription initiation factor TFIID subunit 7
+Macromolecule #17: Transcription initiation factor TFIID subunit 8
+Macromolecule #18: Transcription initiation factor TFIID subunit 9
+Macromolecule #19: Transcription initiation factor TFIID subunit 10
+Macromolecule #20: Transcription initiation factor TFIID subunit 12
+Macromolecule #21: Transcription initiation factor IIA subunit 2
+Macromolecule #22: TATA-box-binding protein
+Macromolecule #23: Transcription initiation factor IIA subunit 1
+Macromolecule #24: Transcription initiation factor IIB
+Macromolecule #25: General transcription factor IIF subunit 1
+Macromolecule #26: General transcription factor IIF subunit 2
+Macromolecule #27: General transcription factor IIE subunit 1
+Macromolecule #28: Transcription initiation factor IIE subunit beta
+Macromolecule #31: Transcription initiation factor TFIID subunit 3
+Macromolecule #32: Transcription initiation factor TFIID subunit 11
+Macromolecule #33: Transcription initiation factor TFIID subunit 13
+Macromolecule #34: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #35: DNA-directed RNA polymerase subunit beta
+Macromolecule #36: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #37: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #38: DNA-directed RNA polymerase II subunit E
+Macromolecule #39: DNA-directed RNA polymerase II subunit F
+Macromolecule #40: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #41: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #42: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #43: RPB10
+Macromolecule #44: RNA_pol_L_2 domain-containing protein
+Macromolecule #45: RPB12
+Macromolecule #29: DNA (71-MER)
+Macromolecule #30: DNA (71-MER)
+Macromolecule #46: ZINC ION
+Macromolecule #47: IRON/SULFUR CLUSTER
+Macromolecule #48: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42939 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |