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- PDB-5x6o: Intact ATR/Mec1-ATRIP/Ddc2 complex -

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Basic information

Entry
Database: PDB / ID: 5x6o
TitleIntact ATR/Mec1-ATRIP/Ddc2 complex
Components
  • DNA damage checkpoint protein LCD1DNA repair
  • Serine/threonine-protein kinase MEC1
KeywordsTRANSFERASE/DNA BINDING PROTEIN / ATR/Mec1 / Kinase / Dimeric / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homologyPIK-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 / histone phosphorylation / telomere maintenance via telomerase / 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 sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / 3.9 Å resolution
AuthorsWang, X. / Ran, T. / Cai, G.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 22, 2017 / Release: Dec 20, 2017

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Assembly

Deposited unit
C: Serine/threonine-protein kinase MEC1
G: DNA damage checkpoint protein LCD1


Theoretical massNumber of molelcules
Total (without water)360,2142
Polyers360,2142
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)8670
ΔGint (kcal/M)-45
Surface area (Å2)137250

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Components

#1: Protein/peptide Serine/threonine-protein kinase MEC1 / ATR homolog / DNA-damage checkpoint kinase MEC1 / Mitosis entry checkpoint protein 1


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 DNA damage checkpoint protein LCD1 / DNA repair / DNA damage checkpoint protein 2 / Lethal / checkpoint-defective / DNA damage-sensitive protein 1


Mass: 86533.594 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04377

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATR/Mec1-ATRIP/Ddc2 / Type: COMPLEX / Details: ATR/Mec1 "butterfly" / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 8
SpecimenDetails: ATR/Mec1 "butterfly" / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NONE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2247: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63132 / Symmetry type: POINT
Least-squares processHighest resolution: 3.9 Å
Number of atoms included #1Total: 20282
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719569
ELECTRON MICROSCOPYf_angle_d1.00526595
ELECTRON MICROSCOPYf_dihedral_angle_d11.84411819
ELECTRON MICROSCOPYf_chiral_restr0.0593218
ELECTRON MICROSCOPYf_plane_restr0.0053431
Refine LS shellHighest 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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