+Open data
-Basic information
Entry | Database: PDB / ID: 5x6o | ||||||||||||
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Title | Intact ATR/Mec1-ATRIP/Ddc2 complex | ||||||||||||
Components |
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Keywords | TRANSFERASE/DNA BINDING PROTEIN / ATR/Mec1 / Kinase / Dimeric / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN complex | ||||||||||||
Function / homology | Function and homology information ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / signal transduction in response to DNA damage / telomere maintenance ...ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / telomere maintenance via telomerase / signal transduction in response to DNA damage / telomere maintenance / DNA damage checkpoint signaling / establishment of protein localization / chromatin organization / chromosome / DNA recombination / DNA replication / damaged DNA binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Wang, X. / Ran, T. / Cai, G. | ||||||||||||
Funding support | China, 3items
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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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5x6o.cif.gz | 476.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6o.ent.gz | 364.1 KB | Display | PDB format |
PDBx/mmJSON format | 5x6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x6o_validation.pdf.gz | 993.9 KB | Display | wwPDB validaton report |
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Full document | 5x6o_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5x6o_validation.xml.gz | 76.3 KB | Display | |
Data in CIF | 5x6o_validation.cif.gz | 114.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6o ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6o | HTTPS FTP |
-Related structure data
Related structure data | 6708MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 273680.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P38111, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 86533.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q04377 |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ATR/Mec1-ATRIP/Ddc2 / Type: COMPLEX / Details: ATR/Mec1 "butterfly" / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES / Details: ATR/Mec1 "butterfly" |
EM staining | Type: NONE / Material: Uranyl Formate |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2247: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63132 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.9 Å | ||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 20282 | ||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Resolution: 3.9→4.001 Å / Total num. of bins used: 20
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