+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9306 | |||||||||
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Title | Human TFIID bound to promoter DNA and TFIIA | |||||||||
Map data | Primary map | |||||||||
Sample |
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Keywords | Transcription / DNA / Nuclear / transcription-dna complex | |||||||||
Function / homology | Function and homology information spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 ...spermine transport / negative regulation of MHC class I biosynthetic process / P-TEFb complex binding / 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 / regulation of cell cycle G1/S phase transition / RNA polymerase transcription factor SL1 complex / 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 / transcription regulator inhibitor activity / nuclear vitamin D receptor binding / RNA polymerase binding / RNA polymerase II general transcription initiation factor binding / limb development / box C/D snoRNP assembly / regulation of fat cell differentiation / nuclear thyroid hormone receptor binding / SAGA complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / inner cell mass cell proliferation / response to L-glutamate / embryonic placenta development / cellular response to ATP / midbrain development / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / TFIIB-class transcription factor 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 / somitogenesis / regulation of DNA repair / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / histone acetyltransferase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / lysine-acetylated histone binding / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / regulation of signal transduction by p53 class mediator / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / RNA Polymerase I Promoter Escape / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / euchromatin Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Patel AB / Louder RK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Science / Year: 2018 Title: Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Authors: Avinash B Patel / Robert K Louder / Basil J Greber / Sebastian Grünberg / Jie Luo / Jie Fang / Yutong Liu / Jeff Ranish / Steve Hahn / Eva Nogales / Abstract: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and ...The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box-binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter. | |||||||||
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_9306.map.gz | 78.4 MB | EMDB map data format | |
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Header (meta data) | emd-9306-v30.xml emd-9306.xml | 39.3 KB 39.3 KB | Display Display | EMDB header |
Images | emd_9306.png | 113.2 KB | ||
Filedesc metadata | emd-9306.cif.gz | 10.9 KB | ||
Others | emd_9306_half_map_1.map.gz emd_9306_half_map_2.map.gz | 171.1 MB 171.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9306 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9306 | HTTPS FTP |
-Validation report
Summary document | emd_9306_validation.pdf.gz | 809.5 KB | Display | EMDB validaton report |
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Full document | emd_9306_full_validation.pdf.gz | 809.1 KB | Display | |
Data in XML | emd_9306_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_9306_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9306 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9306 | HTTPS FTP |
-Related structure data
Related structure data | 6mzmMC 9298C 9299C 9300C 9301C 9302C 9305C 6mzcC 6mzdC 6mzlC C: citing same article (ref.) M: atomic model generated by this map |
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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_9306.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: em-half-volume P1
File | emd_9306_half_map_1.map | ||||||||||||
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Annotation | em-half-volume_P1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: em-half-volume P2
File | emd_9306_half_map_2.map | ||||||||||||
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Annotation | em-half-volume_P2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : General transcription factor IID
+Supramolecule #1: General transcription factor IID
+Macromolecule #1: Transcription initiation factor TFIID subunit 1, TAF1
+Macromolecule #2: Transcription initiation factor TFIID subunit 2, TAF2
+Macromolecule #3: Transcription initiation factor TFIID subunit 4, TAF4
+Macromolecule #4: Transcription initiation factor TFIID subunit 5,TAF5
+Macromolecule #5: Transcription initiation factor TFIID subunit 6
+Macromolecule #6: Transcription initiation factor TFIID subunit 6
+Macromolecule #7: Transcription initiation factor TFIID subunit 7
+Macromolecule #8: Transcription initiation factor TFIID subunit 8, TAF8
+Macromolecule #9: Transcription initiation factor TFIID subunit 9, TAF9
+Macromolecule #10: Transcription initiation factor TFIID subunit 10
+Macromolecule #11: Transcription initiation factor TFIID subunit 12
+Macromolecule #12: TATA-box-binding protein
+Macromolecule #15: Transcription initiation factor IIA subunit 1
+Macromolecule #16: Transcription initiation factor IIA subunit 2
+Macromolecule #17: Unk
+Macromolecule #13: SCP DNA (80-MER)
+Macromolecule #14: SCP DNA (80-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .2 mg/mL | ||||||||||||||
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Buffer | pH: 7.9 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: BT 4s; BF 15N. |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25180 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |