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Yorodumi- PDB-8gxq: PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gxq | ||||||
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Title | PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state | ||||||
Components |
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Keywords | TRANSCRIPTION / PIC / Mediator / transcription initiation / +1 nucleosome | ||||||
Function / homology | Function and homology information positive regulation of mediator complex assembly / 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 mediator complex assembly / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) Sus scrofa (pig) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.04 Å | ||||||
Authors | Chen, X. / Wang, X. / Liu, W. / Ren, Y. / Qu, X. / Li, J. / Yin, X. / Xu, Y. | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2022 Title: Structures of +1 nucleosome-bound PIC-Mediator complex. Authors: Xizi Chen / Xinxin Wang / Weida Liu / Yulei Ren / Xuechun Qu / Jiabei Li / Xiaotong Yin / Yanhui Xu / Abstract: RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream ...RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gxq.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8gxq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8gxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/8gxq ftp://data.pdbj.org/pub/pdb/validation_reports/gx/8gxq | HTTPS FTP |
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-Related structure data
Related structure data | 34359MC 8gxsC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+DNA chain , 4 types, 4 molecules XYNXNY
+Transcription initiation factor ... , 17 types, 23 molecules BADADBEBDQDODcDdDDDeDEDfDFDiDIDjDJDkDlDLDmDGDH
+Protein , 11 types, 15 molecules EANANENBNFPKPLDPHDHIHJNGNCNDNH
+General transcription factor IIF subunit ... , 2 types, 2 molecules FAFB
+General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules HAHH
+DNA-directed RNA polymerase ... , 8 types, 8 molecules PAPBPCPEPFPIPDPG
+General transcription factor IIH subunit ... , 5 types, 5 molecules HBHCHEHGHF
+DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules PHPJ
+Mediator of RNA polymerase II transcription subunit ... , 24 types, 24 molecules gjnsuadfimqzbcelokrtvwxy
+Isoform 2 of Mediator of RNA polymerase II transcription subunit ... , 2 types, 2 molecules hp
+Non-polymers , 3 types, 21 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Type: COMPLEX / Entity ID: #1-#77 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Sus scrofa (pig) |
Source (recombinant) | Organism: Sus scrofa (pig) |
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 |
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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 5.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26458 / Symmetry type: POINT |