6XP5

Head-Middle module of Mediator


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mediator structure and conformation change.

Zhang, H.Chen, D.H.Mattoo, R.U.H.Bushnell, D.A.Wang, Y.Yuan, C.Wang, L.Wang, C.Davis, R.E.Nie, Y.Kornberg, R.D.

(2021) Mol Cell 81: 1781-1788.e4

  • DOI: https://doi.org/10.1016/j.molcel.2021.01.022
  • Primary Citation of Related Structures:  
    6XP5, 7JMN

  • PubMed 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 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.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, China; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21A [auth U]135Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0029550
UniProt
Find proteins for G0S8E0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4B [auth D]341Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED4CTHT_0037540
UniProt
Find proteins for G0S7Z4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6C [auth F]337Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED6CTHT_0067530
UniProt
Find proteins for G0SGT8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7D [auth G]246Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0064270
UniProt
Find proteins for G0SEM4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9E [auth I]179Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED9CTHT_0016410
UniProt
Find proteins for G0S292 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14F [auth N]1,171Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0057660
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17G [auth Q]634Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED17CTHT_0014540
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31H [auth Z]124Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0015060
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8I [auth H]290Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED8CTHT_0058900
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11J [auth K]238Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED11CTHT_0068270
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18K [auth R]340Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: MED18CTHT_0007510
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Med22L [auth V]169Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0021510
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1M [auth a]736Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0063280
UniProt
Find proteins for G0SEC7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideN [auth b]21Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0063280
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
HEATO [auth c]200Thermochaetoides thermophilaMutation(s): 0 
Sequence Annotations
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references