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- PDB-9iz0: ATM/Tel1 bound to CHK2 peptide -

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Basic information

Entry
Database: PDB / ID: 9iz0
TitleATM/Tel1 bound to CHK2 peptide
Components
  • Serine/threonine-protein kinase tel1
  • VAL-SER-THR-GLN-GLU-LEU-TYR-SER
KeywordsSTRUCTURAL PROTEIN / ATM / Tel1 / activation / AMPPNP / MMS-induced / DNA
Function / homology
Function and homology information


spatial regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of initiation of premeiotic DNA replication / Regulation of TP53 Activity through Phosphorylation / Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / histone H2A kinase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling ...spatial regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of initiation of premeiotic DNA replication / Regulation of TP53 Activity through Phosphorylation / Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / histone H2A kinase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / telomere maintenance / DNA damage checkpoint signaling / double-strand break repair / chromosome / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol
Similarity search - Function
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase tel1
Similarity search - Component
Biological speciesHomo sapiens (human)
Schizosaccharomyces pombe 972h- (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsWang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Asymmetric activation of dimeric ATM/Tel1 kinase.
Authors: Po Wang / Zexuan Zheng / Guangxian Wang / Zhanpeng Zhao / Dong Qian / Gang Cai / Xuejuan Wang /
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: VAL-SER-THR-GLN-GLU-LEU-TYR-SER
A: Serine/threonine-protein kinase tel1
B: Serine/threonine-protein kinase tel1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)656,9675
Polymers655,9543
Non-polymers1,0122
Water00
1


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

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Components

#1: Protein/peptide VAL-SER-THR-GLN-GLU-LEU-TYR-SER


Mass: 925.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Serine/threonine-protein kinase tel1 / ATM homolog / DNA-damage checkpoint kinase tel1 / Telomere length regulation protein 1


Mass: 327514.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: tel1, SPCC23B6.03c / Production host: Schizosaccharomyces pombe (fission yeast)
References: UniProt: O74630, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
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: ATM/Tel1 bound to CHK2 peptide / Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
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 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64713 / Symmetry type: POINT
RefinementHighest resolution: 3.63 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332533
ELECTRON MICROSCOPYf_angle_d0.63644537
ELECTRON MICROSCOPYf_dihedral_angle_d5.2345027
ELECTRON MICROSCOPYf_chiral_restr0.045538
ELECTRON MICROSCOPYf_plane_restr0.0045850

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