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- EMDB-2635: Electron microscopy of human transcriptional Mediator -

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Basic information

Entry
Database: EMDB / ID: EMD-2635
TitleElectron microscopy of human transcriptional Mediator
Map dataNegative-stained reconstruction of human transcriptional Mediator
Sample
  • Sample: human transcriptional Mediator
  • Protein or peptide: human transcriptional Mediator
Keywordshuman / transcription / Mediator / Med26 / RNAPII / MED
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsTsai KT / Tomomori-Sato C / Sato S / Conaway RC / Conaway JW / Asturias FJ
CitationJournal: Cell / Year: 2014
Title: Subunit architecture and functional modular rearrangements of the transcriptional mediator complex.
Authors: Kuang-Lei Tsai / Chieri Tomomori-Sato / Shigeo Sato / Ronald C Conaway / Joan W Conaway / Francisco J Asturias /
Abstract: The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA ...The multisubunit Mediator, comprising ∼30 distinct proteins, plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery. Efforts to uncover the Mediator mechanism have been hindered by a poor understanding of its structure, subunit organization, and conformational rearrangements. By overcoming biochemical and image analysis hurdles, we obtained accurate EM structures of yeast and human Mediators. Subunit localization experiments, docking of partial X-ray structures, and biochemical analyses resulted in comprehensive mapping of yeast Mediator subunits and a complete reinterpretation of our previous Mediator organization model. Large-scale Mediator rearrangements depend on changes at the interfaces between previously described Mediator modules, which appear to be facilitated by factors conducive to transcription initiation. Conservation across eukaryotes of Mediator structure, subunit organization, and RNA polymerase II interaction suggest conservation of fundamental aspects of the Mediator mechanism.
History
DepositionApr 23, 2014-
Header (metadata) releaseMay 28, 2014-
Map releaseMay 28, 2014-
UpdateJun 18, 2014-
Current statusJun 18, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2635_hME...

Downloads & links

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Map

FileDownload / File: emd_2635.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stained reconstruction of human transcriptional Mediator
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 126 pix.
= 126. Å		1 Å/pix.
x 126 pix.
= 126. Å		1 Å/pix.
x 126 pix.
= 126. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.111
CCP4 map header111
EM Navigator Movie #14.24.24.2
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.03 / Movie #1: 0.022
Minimum - Maximum-0.02535142 - 0.09886546
Average (Standard dev.)0.00069716 (±0.00628022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions126126126
Spacing126126126
CellA=B=C: 126.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z126126126
origin x/y/z0.0000.0000.000
length x/y/z126.000126.000126.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS126126126
D min/max/mean-0.0250.0990.001

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Supplemental data

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Sample components

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Entire : human transcriptional Mediator

EntireName: human transcriptional Mediator
Components
  • Sample: human transcriptional Mediator
  • Protein or peptide: human transcriptional Mediator

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Supramolecule #1000: human transcriptional Mediator

SupramoleculeName: human transcriptional Mediator / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: human transcriptional Mediator

MacromoleculeName: human transcriptional Mediator / type: protein_or_peptide / ID: 1 / Name.synonym: hMED / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa-S3 / synonym: Human
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 0.75% w/v uranyl formate for 30 seconds
GridDetails: 400 mesh gold grid with thin carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DateJun 10, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: EMAN2/SPARX / Number images used: 2025

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