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- PDB-5yz0: Cryo-EM Structure of human ATR-ATRIP complex -

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Basic information

Entry
Database: PDB / ID: 5yz0
TitleCryo-EM Structure of human ATR-ATRIP complex
Components
  • ATR-interacting protein
  • Serine/threonine-protein kinase ATR
KeywordsCELL 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 / establishment of protein-containing complex localization to telomere / nuclear membrane disassembly / MutLalpha complex binding / response to arsenic-containing substance / regulation of double-strand break repair / mitotic G2/M transition checkpoint ...ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / MutSalpha complex binding / establishment of protein-containing complex localization to telomere / nuclear membrane disassembly / MutLalpha complex binding / response to arsenic-containing substance / regulation of double-strand break repair / mitotic G2/M transition checkpoint / positive regulation of DNA damage response, signal transduction by p53 class mediator / nucleobase-containing compound metabolic process / protein localization to chromosome, telomeric region / HDR through Single Strand Annealing (SSA) / K63-linked polyubiquitin modification-dependent protein binding / Impaired BRCA2 binding to RAD51 / negative regulation of DNA replication / replication fork processing / site of DNA damage / 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 / response to mechanical stimulus / regulation of cellular response to heat / positive regulation of telomere maintenance via telomerase / Meiotic synapsis / telomere maintenance / DNA damage checkpoint signaling / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / G2/M DNA damage checkpoint / cellular response to gamma radiation / PML body / cellular response to UV / nuclear envelope / double-strand break repair / peptidyl-serine phosphorylation / chromosome / Processing of DNA double-strand break ends / protein autophosphorylation / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / Golgi apparatus / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATR-interacting protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT ...ATR-interacting protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase ATR / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsRao, Q. / Liu, M. / Tian, Y. / Wu, Z. / Wang, H. / Wang, J. / Xu, Y.
Funding support China, 7items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500700 China
Ministry of Science and Technology (China)2016YFA0501100 China
Strategic Priority Research Program of Chinese Academy of Sciences(CAS))XDB08000000 China
National Natural Science Foundation of ChinaU1432242 China
National Natural Science Foundation of China31425008 China
National Natural Science Foundation of China91419301 China
Beijing Municipal Science & Technology CommissionZ161100000116034 China
CitationJournal: 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
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ATR
B: Serine/threonine-protein kinase ATR
C: ATR-interacting protein
D: ATR-interacting protein


Theoretical massNumber of molelcules
Total (without water)775,3954
Polymers775,3954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine/threonine-protein kinase ATR / Ataxia telangiectasia and Rad3-related protein / FRAP-related protein 1


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 ATR-interacting protein / ATM and Rad3-related-interacting 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATR-ATRIP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 700 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266218 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00833868
ELECTRON MICROSCOPYf_angle_d1.20646538
ELECTRON MICROSCOPYf_dihedral_angle_d7.21120396
ELECTRON MICROSCOPYf_chiral_restr0.055882
ELECTRON MICROSCOPYf_plane_restr0.0076264

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