- EMDB-31207: TFIID-based PIC-Mediator holo-complex in fully-assembled state (h... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-31207
Title
TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
Map data
TFIID-based PIC-MED holo-complex (deletion of MED1-IDR) in assembled state (hPIC-MED)
Sample
Complex: TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
Protein or peptide: x 68 types
DNA: x 2 types
Ligand: x 3 types
Function / homology
Function and homology information
positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / MMXD complex / androgen biosynthetic process / positive regulation of G0 to G1 transition ...positive regulation of T cell extravasation / negative regulation of smooth muscle cell differentiation / spermine transport / negative regulation of MHC class I biosynthetic process / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / MMXD complex / androgen biosynthetic process / positive regulation of G0 to G1 transition / core TFIIH complex portion of holo TFIIH complex / retinal pigment epithelium development / mammary gland branching involved in thelarche / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / G0 to G1 transition / pre-snoRNP complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / thyroid hormone receptor signaling pathway / negative regulation of protein autoubiquitination / central nervous system myelin formation / transcription factor TFTC complex / positive regulation of mitotic recombination / regulation of vitamin D receptor signaling pathway / core mediator complex / positive regulation of core promoter binding / meiotic sister chromatid cohesion / negative regulation of MHC class II biosynthetic process / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / cyclin-dependent protein kinase activating kinase holoenzyme complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / 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 / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / 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 I core promoter sequence-specific DNA binding / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / ventricular trabecula myocardium morphogenesis / hepatocyte differentiation / thyroid hormone generation / nuclear retinoic acid receptor binding / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / positive regulation of response to cytokine stimulus / mediator complex / positive regulation of androgen receptor activity / positive regulation of keratinocyte differentiation / maintenance of protein location in nucleus / Generic Transcription Pathway / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex Similarity search - Function
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
Deposition
Apr 16, 2021
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Header (metadata) release
May 26, 2021
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Map release
May 26, 2021
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Update
Jun 16, 2021
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Current status
Jun 16, 2021
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Macromolecule #30: General transcription factor IIH subunit 5
Macromolecule
Name: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)
Organism: Homo sapiens (human)
Molecular weight
Theoretical: 8.060362 KDa
Recombinant expression
Organism: Homo sapiens (human)
Sequence
String:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K
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Macromolecule #31: General transcription and DNA repair factor IIH helicase subunit XPB
Macromolecule
Name: General transcription and DNA repair factor IIH helicase subunit XPB type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Macromolecule #32: General transcription and DNA repair factor IIH helicase subunit XPD
Macromolecule
Name: General transcription and DNA repair factor IIH helicase subunit XPD type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
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