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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | PIC-Mediator in complex with +1 nucleosome (T50N) | |||||||||
![]() | PIC-Mediator in complex with plus 1 nucleosome (T50N) | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.12 Å | |||||||||
![]() | Chen X / Wang X / Liu W / Ren Y / Qu X / Li J / Yin X / Xu Y | |||||||||
Funding support | 1 items
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 71.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.5 KB 37.5 KB | Display Display | ![]() |
Images | ![]() | 47.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 35.4 MB 71.6 MB 47.4 MB 35.9 MB 71.1 MB 71.5 MB 13.6 MB 13.7 MB 69.9 MB 35.4 MB 35.4 MB 65.5 MB 65.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 717 KB | Display | ![]() |
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Full document | ![]() | 716.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | PIC-Mediator in complex with plus 1 nucleosome (T50N) | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Additional map: Nucleosome of PIC-Mediator in complex with plus 1...
+Additional map: PIC-Mediator in complex with plus 1 nucleosome (T50N)...
+Additional map: PIC core of the T50N-bound PIC-Mediator
+Additional map: Nucleosome of PIC-Mediator in complex with plus 1...
+Additional map: PIC-Mediator in complex with plus 1 nucleosome (T50N)...
+Additional map: PIC-Mediator in complex with plus 1 nucleosome (T50N)...
+Additional map: TFIID of the T50N-bound PIC-Mediator
+Additional map: TFIIH of the T50N-bound PIC-Mediator
+Additional map: Mediator of the T50N-bound PIC-Mediator
+Additional map: Nucleosome of PIC-Mediator in complex with plus 1...
+Additional map: Nucleosome of PIC-Mediator in complex with plus 1...
+Half map: #2
+Half map: #1
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Sample components
-Entire : PIC, Mediator, transcription initiation, +1 nucleosome
Entire | Name: PIC, Mediator, transcription initiation, +1 nucleosome |
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Components |
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-Supramolecule #1: PIC, Mediator, transcription initiation, +1 nucleosome
Supramolecule | Name: PIC, Mediator, transcription initiation, +1 nucleosome type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15415 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |