+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 / hepatocyte differentiation / positive regulation of response to cytokine stimulus / 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 / hepatocyte differentiation / positive regulation of response to cytokine stimulus / maintenance of protein location in nucleus / C2H2 zinc finger domain binding / RNA polymerase binding / box C/D snoRNP assembly / SAGA complex / limb development / transcription preinitiation complex / regulation of fat cell differentiation / inner cell mass cell proliferation / response to L-glutamate / 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 / regulation of RNA splicing / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / MLL1 complex / negative regulation of cell cycle / somitogenesis / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / response to interleukin-1 / male germ cell nucleus / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / nuclear estrogen receptor binding / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / multicellular organism growth / response to organic cyclic compound / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / p53 binding / actin cytoskeleton / HATs acetylate histones / ATPase binding / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / cell differentiation / transcription cis-regulatory region binding / protein stabilization / Ub-specific processing proteases / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / DNA damage response / chromatin binding / regulation of DNA-templated transcription / negative regulation of apoptotic process / chromatin / regulation of transcription by RNA polymerase II / 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 |
-Validation report
Summary document | emd_9298_validation.pdf.gz | 671 KB | Display | EMDB validaton report |
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Full document | emd_9298_full_validation.pdf.gz | 670.5 KB | Display | |
Data in XML | emd_9298_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_9298_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9298 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266328 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |