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- PDB-23fc: Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1 -

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Basic information

Entry
Database: PDB / ID: 23fc
TitleCryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1
Components
  • (Serine/threonine-protein kinase ...) x 2
  • ATR-interacting protein
KeywordsNUCLEAR PROTEIN / ATR / TopBp1 / Chk1 / DNA repair
Function / homology
Function and homology information


ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / nuclear membrane disassembly / histone H2AXS139 kinase activity / negative regulation of mitotic nuclear division / apoptotic process involved in development / negative regulation of G0 to G1 transition ...ATR-ATRIP complex / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / establishment of protein-containing complex localization to telomere / MutSalpha complex binding / nuclear membrane disassembly / histone H2AXS139 kinase activity / negative regulation of mitotic nuclear division / apoptotic process involved in development / negative regulation of G0 to G1 transition / histone H3T11 kinase activity / MutLalpha complex binding / regulation of mitotic centrosome separation / mitotic G2/M transition checkpoint / response to arsenic-containing substance / regulation of double-strand break repair / nucleobase-containing compound metabolic process / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein localization to chromosome, telomeric region / peptidyl-threonine phosphorylation / inner cell mass cell proliferation / K63-linked polyubiquitin modification-dependent protein binding / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination / nucleus organization / negative regulation of gene expression, epigenetic / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Impaired BRCA2 binding to RAD51 / replication fork processing / replicative senescence / Regulation of HSF1-mediated heat shock response / Presynaptic phase of homologous DNA pairing and strand exchange / response to mechanical stimulus / Activation of ATR in response to replication stress / interstrand cross-link repair / regulation of cellular response to heat / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / site of DNA damage / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / positive regulation of cell cycle / telomere maintenance / DNA damage checkpoint signaling / Meiotic synapsis / regulation of signal transduction by p53 class mediator / replication fork / condensed nuclear chromosome / TP53 Regulates Transcription of DNA Repair Genes / Fanconi Anemia Pathway / cellular response to mechanical stimulus / Signaling by SCF-KIT / cellular response to gamma radiation / G2/M DNA damage checkpoint / PML body / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / G2/M transition of mitotic cell cycle / cellular response to UV / nuclear envelope / double-strand break repair / regulation of cell population proliferation / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / protein kinase activity / DNA replication / non-specific serine/threonine protein kinase / chromatin remodeling / response to xenobiotic stimulus / protein domain specific binding / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / chromatin / Golgi apparatus / protein-containing complex / : / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
ATR-interacting protein / : / Serine/threonine-protein kinase ATR, N-HEAT region / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Checkpoint kinase 1, catalytic domain / : ...ATR-interacting protein / : / Serine/threonine-protein kinase ATR, N-HEAT region / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Checkpoint kinase 1, catalytic domain / : / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase Chk1 / Serine/threonine-protein kinase ATR / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang, L. / Wang, M. / Zhao, L. / Rao, Q. / Wu, H. / Ma, B. / Wang, J. / Zheng, J. / Li, Y. / Xu, Y. ...Wang, L. / Wang, M. / Zhao, L. / Rao, Q. / Wu, H. / Ma, B. / Wang, J. / Zheng, J. / Li, Y. / Xu, Y. / Guo, J. / Cheng, J. / Qiao, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human ATR-ATRIP complex with ATPgammaS and Chk1
Authors: Wang, L. / Wang, M. / Zhao, L. / Rao, Q. / Wu, H. / Ma, B. / Wang, J. / Zheng, J. / Li, Y. / Xu, Y. / Guo, J. / Cheng, J. / Qiao, S.
History
DepositionFeb 4, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: Serine/threonine-protein kinase Chk1
F: Serine/threonine-protein kinase Chk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)779,90216
Polymers778,4966
Non-polymers1,40510
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Serine/threonine-protein kinase ... , 2 types, 4 molecules ABEF

#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 / Production host: Homo sapiens (human)
References: UniProt: Q13535, non-specific serine/threonine protein kinase
#3: Protein/peptide Serine/threonine-protein kinase Chk1 / CHK1 checkpoint homolog / Cell cycle checkpoint kinase / Checkpoint kinase-1


Mass: 1550.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: VKYSSSQPEPRTGL / Source: (synth.) Homo sapiens (human)
References: UniProt: O14757, non-specific serine/threonine protein kinase

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Protein , 1 types, 2 molecules CD

#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 / Production host: Homo sapiens (human) / References: UniProt: Q8WXE1

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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: human ATR-ATRIP complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256654 / Symmetry type: POINT

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