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- PDB-9l4c: ATR Spiral -ATRIP bound with RP-3500 -

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Basic information

Entry
Database: PDB / ID: 9l4c
TitleATR Spiral -ATRIP bound with RP-3500
Components
  • ATR-interacting protein
  • Serine/threonine-protein kinase ATR
KeywordsCELL CYCLE / ATR spiral ATRIP RP-3500
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 / MutLalpha complex binding / regulation of double-strand break repair / response to arsenic-containing substance / mitotic G2/M transition checkpoint ...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 / MutLalpha complex binding / regulation of double-strand break repair / response to arsenic-containing substance / 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 / telomere maintenance / Meiotic synapsis / 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 / chromosome / Processing of DNA double-strand break ends / peptidyl-serine phosphorylation / 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 / DNA replication / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / HEAT repeat profile. / HEAT, type 2 / : / FATC domain / PIK-related kinase, FAT / FAT domain ...ATR-interacting protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / 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: 4.06 Å
AuthorsWang, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Bull (Beijing) / Year: 2025
Title: Molecular architecture and inhibition mechanism of human ATR-ATRIP
Authors: Wang, G. / Wang, P. / Zheng, Z. / Zhang, Q. / Xu, C. / Xu, X. / Jian, L. / Zhao, Z. / Cai, G. / Wang, X.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)775,5266
Polymers775,3954
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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 / 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 / Production host: Homo sapiens (human) / References: UniProt: Q8WXE1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: ATR-ATRIP / Type: CELL / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.16_3549 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77631 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00521562
ELECTRON MICROSCOPYf_angle_d0.70637697
ELECTRON MICROSCOPYf_dihedral_angle_d7.3088911
ELECTRON MICROSCOPYf_chiral_restr0.0372504
ELECTRON MICROSCOPYf_plane_restr0.0034999

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