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- EMDB-34256: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N) -

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Basic information

Entry
Database: EMDB / ID: EMD-34256
TitlePIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)
Map dataPIC-Mediator in complex with plus 1 H2A-containing nucleosome (T40N)
Sample
  • Complex: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.84 Å
AuthorsChen X / Wang X / Liu W / Ren Y / Qu X / Li J / Yin X / Xu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionSep 8, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34256.png

Downloads & links

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Map

FileDownload / File: emd_34256.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPIC-Mediator in complex with plus 1 H2A-containing nucleosome (T40N)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 420 pix.
= 560.28 Å		1.33 Å/pix.
x 420 pix.
= 560.28 Å		1.33 Å/pix.
x 420 pix.
= 560.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.334 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.012726761 - 0.061855257
Average (Standard dev.)0.000102121405 (±0.0046168533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 560.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Nucleosome PIC-Mediator in complex with plus 1 H2A-containing...

Fileemd_34256_additional_1.map
AnnotationNucleosome PIC-Mediator in complex with plus 1 H2A-containing nucleosome (T40N)
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_34256_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_34256_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)

EntireName: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)
Components
  • Complex: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)

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Supramolecule #1: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)

SupramoleculeName: PIC-Mediator in complex with +1 H2A-containing nucleosome (T40N)
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 reconstructionResolution.type: BY AUTHOR / Resolution: 10.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12554
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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