6Z2X

Mec1-Ddc2 (F2244L mutant) in complex with Mg AMP-PNP (State II)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of auto-inhibition and activation of Mec1 ATR checkpoint kinase.

Tannous, E.A.Yates, L.A.Zhang, X.Burgers, P.M.

(2021) Nat Struct Mol Biol 28: 50-61

  • DOI: https://doi.org/10.1038/s41594-020-00522-0
  • Primary Citation of Related Structures:  
    6Z2W, 6Z2X, 6Z3A

  • PubMed Abstract: 

    In response to DNA damage or replication fork stalling, the basal activity of Mec1 ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1 ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg 2+ -AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint protein LCD1A [auth D],
B [auth C]
747Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LCD1DDC2PIE1YDR499W
UniProt
Find proteins for Q04377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04377 
Go to UniProtKB:  Q04377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04377
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase MEC1C [auth E],
D [auth F]
2,368Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: MEC1ESR1SAD3YBR136WYBR1012
EC: 2.7.11.1
UniProt
Find proteins for P38111 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38111 
Go to UniProtKB:  P38111
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38111
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210658/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2020-12-30
    Changes: Structure summary
  • Version 1.3: 2021-01-20
    Changes: Database references
  • Version 1.4: 2021-02-10
    Changes: Database references