+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34215 | |||||||||
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Title | PIC-Mediator in complex with +1 nucleosome (T50N) | |||||||||
Map data | PIC-Mediator in complex with plus 1 nucleosome (T50N) | |||||||||
Sample |
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Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.12 Å | |||||||||
Authors | Chen X / Wang X / Liu W / Ren Y / Qu X / Li J / Yin X / Xu Y | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34215.map.gz | 71.2 MB | EMDB map data format | |
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Header (meta data) | emd-34215-v30.xml emd-34215.xml | 37.5 KB 37.5 KB | Display Display | EMDB header |
Images | emd_34215.png | 47.9 KB | ||
Others | emd_34215_additional_1.map.gz emd_34215_additional_10.map.gz emd_34215_additional_11.map.gz emd_34215_additional_2.map.gz emd_34215_additional_3.map.gz emd_34215_additional_4.map.gz emd_34215_additional_5.map.gz emd_34215_additional_6.map.gz emd_34215_additional_7.map.gz emd_34215_additional_8.map.gz emd_34215_additional_9.map.gz emd_34215_half_map_1.map.gz emd_34215_half_map_2.map.gz | 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 | http://ftp.pdbj.org/pub/emdb/structures/EMD-34215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34215 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34215.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-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: Sus scrofa (pig) |
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15415 |