+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22284 | |||||||||
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Title | Head-Middle module of Mediator | |||||||||
Map data | Head-Middle module of Mediator | |||||||||
Sample |
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Keywords | Transcription | |||||||||
Function / homology | Function and homology information core mediator complex / mediator complex / transcription coregulator activity / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zhang HQ / Chen DC | |||||||||
Citation | Journal: Mol Cell / Year: 2021 Title: Mediator structure and conformation change. Authors: Heqiao Zhang / Dong-Hua Chen / Rayees U H Mattoo / David A Bushnell / Yannan Wang / Chao Yuan / Lin Wang / Chunnian Wang / Ralph E Davis / Yan Nie / Roger D Kornberg / Abstract: Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription ...Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions. | |||||||||
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_22284.map.gz | 398.8 MB | EMDB map data format | |
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Header (meta data) | emd-22284-v30.xml emd-22284.xml | 31.1 KB 31.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22284_fsc.xml | 6.5 KB | Display | FSC data file |
Images | emd_22284.png | 126.2 KB | ||
Filedesc metadata | emd-22284.cif.gz | 8.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22284 | HTTPS FTP |
-Related structure data
Related structure data | 6xp5MC 7jmnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22284.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Head-Middle module of Mediator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Head-Middle module of Mediator
+Supramolecule #1: Head-Middle module of Mediator
+Macromolecule #1: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #2: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #3: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #5: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #6: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #7: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #8: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #9: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #10: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #11: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #12: Med22
+Macromolecule #13: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #14: Unknown peptide
+Macromolecule #15: HEAT
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |