7KPX | pdb_00007kpx

Structure of the yeast CKM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KPX

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 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.

Macromolecule Content 

  • Total Structure Weight: 431.3 kDa 
  • Atom Count: 20,762 
  • Modeled Residue Count: 2,875 
  • Deposited Residue Count: 3,754 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Meiotic mRNA stability protein kinase SSN3555Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt
Find proteins for P39073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39073 
Go to UniProtKB:  P39073
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39073
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase II holoenzyme cyclin-like subunit352Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47821 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47821 
Go to UniProtKB:  P47821
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47821
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 121,427Saccharomyces cerevisiae S288CMutation(s): 0 
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 131,420Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38931 
Go to UniProtKB:  P38931
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38931
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United States13127

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