+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2635 | |||||||||
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Title | Electron microscopy of human transcriptional Mediator | |||||||||
Map data | Negative-stained reconstruction of human transcriptional Mediator | |||||||||
Sample |
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Keywords | human / transcription / Mediator / Med26 / RNAPII / MED | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.0 Å | |||||||||
Authors | Tsai KT / Tomomori-Sato C / Sato S / Conaway RC / Conaway JW / Asturias FJ | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2635.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-2635-v30.xml emd-2635.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | EMD-2635_hMED.jpg | 63.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2635 | HTTPS FTP |
-Validation report
Summary document | emd_2635_validation.pdf.gz | 210.3 KB | Display | EMDB validaton report |
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Full document | emd_2635_full_validation.pdf.gz | 209.5 KB | Display | |
Data in XML | emd_2635_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2635 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2635 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2635.map.gz / Format: CCP4 / Size: 7.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative-stained reconstruction of human transcriptional Mediator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human transcriptional Mediator
Entire | Name: human transcriptional Mediator |
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Components |
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-Supramolecule #1000: human transcriptional Mediator
Supramolecule | Name: human transcriptional Mediator / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: human transcriptional Mediator
Macromolecule | Name: human transcriptional Mediator / type: protein_or_peptide / ID: 1 / Name.synonym: hMED / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa-S3 / synonym: Human |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 0.75% w/v uranyl formate for 30 seconds |
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Grid | Details: 400 mesh gold grid with thin carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Date | Jun 10, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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