3J1O

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Interaction of the mediator head module with RNA polymerase II.

Cai, G.Chaban, Y.L.Imasaki, T.Kovacs, J.A.Calero, G.Penczek, P.A.Takagi, Y.Asturias, F.J.

(2012) Structure 20: 899-910

  • DOI: https://doi.org/10.1016/j.str.2012.02.023
  • Primary Citation of Related Structures:  
    3J1N, 3J1O

  • PubMed Abstract: 

    Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the activity of the preinitiation complex. However, the precise mode of interaction between Mediator and RNA polymerase II (RNAPII), and the mechanism of regulation by Mediator remain elusive. We used cryo-electron microscopy and reconstituted in vitro transcription assays to characterize a transcriptionally-active complex including the Mediator Head module and components of a minimum preinitiation complex (RNAPII, TFIIF, TFIIB, TBP, and promoter DNA). Our results reveal how the Head interacts with RNAPII, affecting its conformation and function.


  • Organizational Affiliation

    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11A [auth H]131Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: MED11YMR112CYM9718.11C
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99278 
Go to UniProtKB:  Q99278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99278
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17B [auth I]484Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB4MED17YER022W
UniProt
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32569 
Go to UniProtKB:  P32569
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32569
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8C [auth J]223Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED8YBR193CYBR1403
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38304 
Go to UniProtKB:  P38304
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38304
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22D [auth K]121Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB6MED22YBR253WYBR1721
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32570 
Go to UniProtKB:  P32570
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32570
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18E [auth L]275Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB5MED18YGR104C
UniProt
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32585 
Go to UniProtKB:  P32585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32585
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20F [auth M]210Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SRB2HRS2MED20YHR041C
UniProt
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34162 
Go to UniProtKB:  P34162
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34162
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6G [auth N]25Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED6MTR32YHR058C
UniProt
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38782 
Go to UniProtKB:  P38782
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38782
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Refinement description