|Entry||Database: PDB / ID: 5x6o|
|Title||Intact ATR/Mec1-ATRIP/Ddc2 complex|
|Keywords||TRANSFERASE/DNA BINDING PROTEIN / ATR/Mec1 / Kinase / Dimeric / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN complex|
|Function / homology||PIK-related kinase, FAT / Phosphatidylinositol 3- and 4-kinases signature 1. / UME (NUC010) domain / FATC domain / FAT domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphatidylinositol 3/4-kinase, conserved site / DNA damage checkpoint protein, Lcd1 / Armadillo-type fold ...PIK-related kinase, FAT / Phosphatidylinositol 3- and 4-kinases signature 1. / UME (NUC010) domain / FATC domain / FAT domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphatidylinositol 3/4-kinase, conserved site / DNA damage checkpoint protein, Lcd1 / Armadillo-type fold / PIK-related kinase / UME domain / Tetratricopeptide-like helical domain superfamily / Protein kinase-like domain superfamily / FATC domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / DNA damage checkpoint protein / Phosphatidylinositol 3- and 4-kinases family profile. / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / E3 ubiquitin ligases ubiquitinate target proteins / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 2. / FAT domain profile. / positive regulation of DNA-dependent DNA replication / telomere maintenance via recombination / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / DNA damage induced protein phosphorylation / telomere maintenance via telomerase / histone phosphorylation / telomere maintenance / nuclear chromosome / DNA damage checkpoint / establishment of protein localization / chromatin organization / DNA recombination / DNA replication / damaged DNA binding / non-specific serine/threonine protein kinase / protein kinase activity / DNA repair / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / Serine/threonine-protein kinase MEC1 / DNA damage checkpoint protein LCD1|
Function and homology information
|Specimen source||Saccharomyces cerevisiae (baker's yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / 3.9 Å resolution|
|Authors||Wang, X. / Ran, T. / Cai, G.|
|Citation||Journal: Science / Year: 2017|
Title: 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP.
Authors: Xuejuan Wang / Tingting Ran / Xuan Zhang / Jiyu Xin / Zhihui Zhang / Tengwei Wu / Weiwu Wang / Gang Cai
Abstract: The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR ...The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR acts together with its partner ATRIP. Using cryo-electron microscopy, we determined the structure of intact Mec1-Ddc2 (the yeast homolog of ATR-ATRIP), which is poised for catalysis, at a resolution of 3.9 angstroms. Mec1-Ddc2 forms a dimer of heterodimers through the PRD and FAT domains of Mec1 and the coiled-coil domain of Ddc2. The PRD and Bridge domains in Mec1 constitute critical regulatory sites. The activation loop of Mec1 is inhibited by the PRD, revealing an allosteric mechanism of kinase activation. Our study clarifies the architecture of ATR-ATRIP and provides a structural framework for the understanding of ATR regulation.
SummaryFull reportAbout validation report
|Date||Deposition: Feb 22, 2017 / Release: Dec 20, 2017|
|Structure viewer||Molecule: |
Downloads & links
C: Serine/threonine-protein kinase MEC1
G: DNA damage checkpoint protein LCD1
|#1: Protein/peptide|| |
Mass: 273680.812 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P38111, non-specific serine/threonine protein kinase
|#2: Protein/peptide|| |
Mass: 86533.594 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04377
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: ATR/Mec1-ATRIP/Ddc2 / Type: COMPLEX / Details: ATR/Mec1 "butterfly" / Entity ID: 1,||Molecular weight||Experimental value: YES||Source (natural)||Organism: Saccharomyces cerevisiae (baker's yeast)||Buffer solution||pH: 8||Specimen||Details: ATR/Mec1 "butterfly" / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES||EM staining||Type: NONE / Material: Uranyl Formate||Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: dev_2247: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63132 / Symmetry type: POINT|
|Least-squares process||Highest resolution: 3.9 Å|
|Number of atoms included #1||Total: 20282|
|Refine LS restraints|
|Refine LS shell||Highest resolution: 3.9 Å / R factor R work: 0.535 / Lowest resolution: 4.001 Å / Number reflection R free: 0 / Number reflection R work: 8779 / Total number of bins used: 20 / Percent reflection obs: 1|
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