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- EMDB-31208: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR) -

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Basic information

Entry
Database: EMDB / ID: EMD-31208
TitleLocal maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Map dataCAK module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Sample
  • Complex: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsChen X / Qi Y / Wang X / Wu Z / Yin X / Li J / Liu W / Xu Y
CitationJournal: 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
DepositionApr 16, 2021-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31208.png

Downloads & links

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Map

FileDownload / File: emd_31208.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCAK module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 480 pix.
= 674.4 Å		1.41 Å/pix.
x 480 pix.
= 674.4 Å		1.41 Å/pix.
x 480 pix.
= 674.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.405 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.37180048 - 1.5423164
Average (Standard dev.)0.0002787044 (±0.01154773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 674.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Mediator module in the TFIID-based PIC-Mediator complex (deletion...

Fileemd_31208_additional_1.map
AnnotationMediator module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Pol II module in the TFIID-based PIC-Mediator complex...

Fileemd_31208_additional_2.map
AnnotationPol II module in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CTD-Mediator in the TFIID-based PIC-Mediator complex (deletion of...

Fileemd_31208_additional_3.map
AnnotationCTD-Mediator in the TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)

EntireName: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
Components
  • Complex: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)

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Supramolecule #1: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)

SupramoleculeName: Local maps of TFIID-based PIC-Mediator complex (deletion of MED1-IDR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#72
Source (natural)Organism: Homo sapiens (human)
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 K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110227
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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