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Yorodumi- EMDB-31208: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31208 | |||||||||
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Title | Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | |||||||||
Map data | CAK module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | |||||||||
Authors | Chen X / Qi Y / Wang X / Wu Z / Yin X / Li J / Liu W / Xu Y | |||||||||
Citation | Journal: Science / Year: 2021 Title: Structures of the human Mediator and Mediator-bound preinitiation complex. Authors: Xizi Chen / Xiaotong Yin / Jiabei Li / Zihan Wu / Yilun Qi / Xinxin Wang / Weida Liu / Yanhui Xu / Abstract: The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26- ...The 1.3-megadalton transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 megadaltons) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31208.map.gz | 15.9 MB | EMDB map data format | |
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Header (meta data) | emd-31208-v30.xml emd-31208.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
Images | emd_31208.png | 49.4 KB | ||
Others | emd_31208_additional_1.map.gz emd_31208_additional_2.map.gz emd_31208_additional_3.map.gz | 227.9 MB 3.1 MB 1.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31208 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31208 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31208.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CAK module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.405 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Mediator module in the TFIID-based PIC-Mediator complex (deletion...
File | emd_31208_additional_1.map | ||||||||||||
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Annotation | Mediator module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Pol II module in the TFIID-based PIC-Mediator complex...
File | emd_31208_additional_2.map | ||||||||||||
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Annotation | Pol II module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: CTD-Mediator in the TFIID-based PIC-Mediator complex (deletion of...
File | emd_31208_additional_3.map | ||||||||||||
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Annotation | CTD-Mediator in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Entire | Name: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR) |
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Components |
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-Supramolecule #1: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Supramolecule | Name: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#72 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110227 |