+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9298 | |||||||||
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Title | Human TFIID BC core | |||||||||
Map data | primary map | |||||||||
Sample |
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Keywords | Transcription / DNA / Nuclear | |||||||||
Function / homology | Function and homology information SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus ...SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / transcription factor TFTC complex / SLIK (SAGA-like) complex / positive regulation of response to cytokine stimulus / hepatocyte differentiation / maintenance of protein location in nucleus / C2H2 zinc finger domain binding / box C/D snoRNP assembly / SAGA complex / RNA polymerase binding / limb development / transcription preinitiation complex / regulation of fat cell differentiation / response to L-glutamate / inner cell mass cell proliferation / 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 / MLL1 complex / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / 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 / regulation of DNA repair / somitogenesis / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / male germ cell nucleus / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / G1/S transition of mitotic cell cycle / multicellular organism growth / mRNA transcription by RNA polymerase II / response to organic cyclic compound / G2/M transition of mitotic cell cycle / actin cytoskeleton / p53 binding / HATs acetylate histones / ATPase binding / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / cell differentiation / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / Ub-specific processing proteases / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / apoptotic process / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 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_9298.map.gz | 56.1 MB | EMDB map data format | |
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Header (meta data) | emd-9298-v30.xml emd-9298.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
Images | emd_9298.png | 98.8 KB | ||
Filedesc metadata | emd-9298.cif.gz | 9 KB | ||
Others | emd_9298_half_map_1.map.gz emd_9298_half_map_2.map.gz | 71.1 MB 71.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9298 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9298 | HTTPS FTP |
-Related structure data
Related structure data | 6mzcMC 9299C 9300C 9301C 9302C 9305C 9306C 6mzdC 6mzlC 6mzmC 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_9298.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: half-volume P1
File | emd_9298_half_map_1.map | ||||||||||||
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Annotation | half-volume_P1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-volume P2
File | emd_9298_half_map_2.map | ||||||||||||
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Annotation | 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 2
+Macromolecule #2: Transcription initiation factor TFIID subunit 4
+Macromolecule #3: Transcription initiation factor TFIID subunit 5
+Macromolecule #4: Transcription initiation factor TFIID subunit 6
+Macromolecule #5: Transcription initiation factor TFIID subunit 6
+Macromolecule #6: Transcription initiation factor TFIID subunit 8
+Macromolecule #7: Transcription initiation factor TFIID subunit 9
+Macromolecule #8: Transcription initiation factor TFIID subunit 10
+Macromolecule #9: Transcription initiation factor TFIID subunit 12
+Macromolecule #10: poly(UNK)
-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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Grid | Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #0 - Film thickness: 25 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.05 kPa / Details: Treated with PEI | ||||||||||||||||
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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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 |
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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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266328 |