7KPW

Structure of the H-lobe of yeast CKM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 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

Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.

Li, Y.C.Chao, T.C.Kim, H.J.Cholko, T.Chen, S.F.Li, G.Snyder, L.Nakanishi, K.Chang, C.E.Murakami, K.Garcia, B.A.Boyer, T.G.Tsai, K.L.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd4484
  • Primary Citation of Related Structures:  
    7KPV, 7KPW, 7KPX

  • PubMed Abstract: 

    The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 12A [auth C]1,427Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRB8GIG1MED12NUT6SSN5YCR081WYCR81W/YCR80W
UniProt
Find proteins for P25648 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25648 
Go to UniProtKB:  P25648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25648
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references