+Open data
-Basic information
Entry | Database: PDB / ID: 5yz0 | ||||||||||||||||||||||||
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Title | Cryo-EM Structure of human ATR-ATRIP complex | ||||||||||||||||||||||||
Components |
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Keywords | CELL CYCLE / cryo-EM / ATR-ATRIP / DNA damnage response | ||||||||||||||||||||||||
Function / homology | Function and homology information ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / MutSalpha complex binding / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / response to xenobiotic stimulus => GO:0009410 / multicellular organism development / MutLalpha complex binding / regulation of double-strand break repair ...ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / MutSalpha complex binding / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / response to xenobiotic stimulus => GO:0009410 / multicellular organism development / MutLalpha complex binding / regulation of double-strand break repair / nucleobase-containing compound metabolic process / protein localization to chromosome, telomeric region / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of DNA replication / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / Regulation of HSF1-mediated heat shock response / interstrand cross-link repair / Activation of ATR in response to replication stress / regulation of cellular response to heat / positive regulation of telomere maintenance via telomerase / Meiotic synapsis / telomere maintenance / DNA damage checkpoint signaling / regulation of signal transduction by p53 class mediator / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / G2/M DNA damage checkpoint / PML body / cellular response to gamma radiation / cellular response to UV / chromosome / Processing of DNA double-strand break ends / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / DNA replication / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||||||||||||||
Authors | Rao, Q. / Liu, M. / Tian, Y. / Wu, Z. / Wang, H. / Wang, J. / Xu, Y. | ||||||||||||||||||||||||
Funding support | China, 7items
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Citation | Journal: Cell Res / Year: 2018 Title: Cryo-EM structure of human ATR-ATRIP complex. Authors: Qinhui Rao / Mengjie Liu / Yuan Tian / Zihan Wu / Yuhan Hao / Lei Song / Zhaoyu Qin / Chen Ding / Hong-Wei Wang / Jiawei Wang / Yanhui Xu / Abstract: ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, ...ATR (ataxia telangiectasia-mutated and Rad3-related) protein kinase and ATRIP (ATR-interacting protein) form a complex and play a critical role in response to replication stress and DNA damage. Here, we determined the cryo-electron microscopy (EM) structure of the human ATR-ATRIP complex at 4.7 Å resolution and built an atomic model of the C-terminal catalytic core of ATR (residues 1 521-2 644) at 3.9 Å resolution. The complex adopts a hollow "heart" shape, consisting of two ATR monomers in distinct conformations. The EM map for ATRIP reveals 14 HEAT repeats in an extended "S" shape. The conformational flexibility of ATR allows ATRIP to properly lock the N-termini of the two ATR monomers to favor ATR-ATRIP complex formation and functional diversity. The isolated "head-head" and "tail-tail" each adopts a pseudo 2-fold symmetry. The catalytic pockets face outward and substrate access is not restricted by inhibitory elements. Our studies provide a structural basis for understanding the assembly of the ATR-ATRIP complex and a framework for characterizing ATR-mediated DNA repair pathways. | ||||||||||||||||||||||||
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 | 5yz0.cif.gz | 845.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yz0.ent.gz | 639.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yz0_validation.pdf.gz | 806.7 KB | Display | wwPDB validaton report |
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Full document | 5yz0_full_validation.pdf.gz | 917.2 KB | Display | |
Data in XML | 5yz0_validation.xml.gz | 130.6 KB | Display | |
Data in CIF | 5yz0_validation.cif.gz | 209.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yz0 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yz0 | HTTPS FTP |
-Related structure data
Related structure data | 6862MC 6863C 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: 301756.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATR, FRP1 / Cell line (production host): 293F / Production host: Homo sapiens (human) References: UniProt: Q13535, non-specific serine/threonine protein kinase #2: Protein | Mass: 85940.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATRIP, AGS1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q8WXE1 |
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-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-ATRIP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 700 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: 293F |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266218 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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