+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9306 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human TFIID bound to promoter DNA and TFIIA | |||||||||
Map data | Primary map | |||||||||
Sample |
| |||||||||
Keywords | Transcription / DNA / Nuclear / transcription-dna complex | |||||||||
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 / TFIIH-class transcription factor complex binding / pre-snoRNP complex / 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 / TFIIH-class transcription factor complex binding / pre-snoRNP complex / 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 / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / 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 androgen receptor activity / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / male pronucleus / female pronucleus / SAGA complex / nuclear vitamin D receptor binding / transcription regulator inhibitor activity / RNA polymerase binding / RNA polymerase II general transcription initiation factor binding / limb development / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cellular response to ATP / RNA Polymerase I Transcription Termination / regulation of fat cell differentiation / response to L-glutamate / inner cell mass cell proliferation / histone acetyltransferase binding / midbrain development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / regulation of RNA splicing / 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 / ubiquitin conjugating enzyme activity / MLL1 complex / RNA Polymerase I Transcription Initiation / transcription initiation at RNA polymerase I promoter / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / P-TEFb complex binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell cycle / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / RNA polymerase II core promoter sequence-specific DNA binding / intracellular estrogen receptor signaling pathway / regulation of DNA repair / transcription by RNA polymerase III / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / histone acetyltransferase activity / ovarian follicle development / RNA polymerase II preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / regulation of signal transduction by p53 class mediator / nuclear estrogen receptor binding / promoter-specific chromatin binding / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / peptidyl-threonine phosphorylation / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / multicellular organism growth / lysine-acetylated histone binding / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression 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
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
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 | |
---|---|---|---|---|
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 |
-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 |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: em-half-volume P1
File | emd_9306_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | em-half-volume_P1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: em-half-volume P2
File | emd_9306_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | em-half-volume_P2 | ||||||||||||
Projections & Slices |
| ||||||||||||
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .2 mg/mL | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.9 Component:
| ||||||||||||||
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 |
---|---|
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 FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
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 |