[English] 日本語
Yorodumi- PDB-7ena: TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ena | ||||||
---|---|---|---|---|---|---|---|
Title | TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / mediator / preinitiation complex / transcription initiation | ||||||
Function / homology | Function and homology information positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / enucleate erythrocyte development / spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of type II interferon-mediated signaling pathway / mammary gland branching involved in thelarche / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / MMXD complex / retinal pigment epithelium development / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / G0 to G1 transition / TFIIH-class transcription factor complex binding / pre-snoRNP complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / thyroid hormone mediated signaling pathway / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / negative regulation of protein autoubiquitination / transcription factor TFTC complex / positive regulation of mitotic recombination / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / hair cell differentiation / negative regulation of MHC class II biosynthetic process / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / SLIK (SAGA-like) complex / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / nuclear DNA-directed RNA polymerase complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / positive regulation of response to cytokine stimulus / mediator complex / nuclear retinoic acid receptor binding / ventricular trabecula myocardium morphogenesis / hepatocyte differentiation / maintenance of protein location in nucleus / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / thyroid hormone generation / 5'-3' DNA helicase activity / positive regulation of androgen receptor activity / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of keratinocyte differentiation / Generic Transcription Pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ena.cif.gz | 4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ena.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ena.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/7ena ftp://data.pdbj.org/pub/pdb/validation_reports/en/7ena | HTTPS FTP |
---|
-Related structure data
Related structure data | 31204MC 7emfC 7encC 7enjC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+Protein , 10 types, 10 molecules 089DPDQPAPJPKPLEA
+Transcription initiation factor ... , 16 types, 22 molecules DOBADADBDDDdDEDeDFDfDGDHDIDiDJDjDLDlDcDkDmEB
+General transcription factor IIF subunit ... , 2 types, 2 molecules FAFB
+DNA-directed RNA ... , 8 types, 8 molecules PBPCPDPEPFPGPHPI
+General transcription factor IIH subunit ... , 5 types, 5 molecules 12345
+General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 67
+Mediator of RNA polymerase II transcription subunit ... , 23 types, 23 molecules ceblmadfgijknoqrstuvzxw
+Isoform 2 of Mediator of RNA polymerase II transcription subunit ... , 2 types, 2 molecules hp
+DNA chain , 2 types, 2 molecules XY
+Non-polymers , 3 types, 18 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
---|---|
3D reconstruction | Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48654 / Symmetry type: POINT |