+Open data
-Basic information
Entry | Database: PDB / ID: 5np1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Open protomer of human ATM (Ataxia telangiectasia mutated) | |||||||||
Components | Serine-protein kinase ATM | |||||||||
Keywords | TRANSFERASE / FAT / MRN / DNA-repair / HEAT-repeats | |||||||||
Function / homology | Function and homology information positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / regulation of microglial cell activation ...positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / regulation of microglial cell activation / meiotic telomere clustering / pre-B cell allelic exclusion / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / male meiotic nuclear division / histone mRNA catabolic process / female meiotic nuclear division / pexophagy / cellular response to X-ray / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / DNA double-strand break processing / lipoprotein catabolic process / V(D)J recombination / regulation of autophagosome assembly / oocyte development / Impaired BRCA2 binding to PALB2 / reciprocal meiotic recombination / DNA repair complex / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / 1-phosphatidylinositol-3-kinase activity / response to ionizing radiation / mitotic spindle assembly checkpoint signaling / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of B cell proliferation / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / positive regulation of cell adhesion / replicative senescence / Regulation of HSF1-mediated heat shock response / signal transduction in response to DNA damage / somitogenesis / regulation of cellular response to heat / cellular response to retinoic acid / ovarian follicle development / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Pexophagy / telomere maintenance / post-embryonic development / thymus development / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / regulation of autophagy / Nonhomologous End-Joining (NHEJ) / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / cellular response to reactive oxygen species / brain development / multicellular organism growth / HDR through Homologous Recombination (HRR) / Regulation of TP53 Activity through Methylation / cellular senescence / cellular response to gamma radiation / spindle / double-strand break repair via nonhomologous end joining / Regulation of TP53 Degradation / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / double-strand break repair / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / heart development / peptidyl-serine phosphorylation / site of double-strand break / cytoplasmic vesicle / Regulation of TP53 Activity through Phosphorylation / neuron apoptotic process / regulation of apoptotic process / protein autophosphorylation / response to hypoxia / regulation of cell cycle / non-specific serine/threonine protein kinase / positive regulation of cell migration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Baretic, D. / Pollard, H.K. / Fisher, D.I. / Johnson, C.M. / Santhanam, B. / Truman, C.M. / Kouba, T. / Fersht, A.R. / Phillips, C. / Williams, R.L. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Sci Adv / Year: 2017 Title: Structures of closed and open conformations of dimeric human ATM. Authors: Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams / Abstract: ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, ...ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5np1.cif.gz | 379.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5np1.ent.gz | 245.7 KB | Display | PDB format |
PDBx/mmJSON format | 5np1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5np1_validation.pdf.gz | 792.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5np1_full_validation.pdf.gz | 887.3 KB | Display | |
Data in XML | 5np1_validation.xml.gz | 70.8 KB | Display | |
Data in CIF | 5np1_validation.cif.gz | 113.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/5np1 ftp://data.pdbj.org/pub/pdb/validation_reports/np/5np1 | HTTPS FTP |
-Related structure data
Related structure data | 3672MC 3668C 3669C 3670C 3671C 3673C 5np0C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 352393.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: ATM / Plasmid: pDEST12.2-OriP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: Q13315, non-specific serine/threonine protein kinase |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.705 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pDEST12.2-OriP | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was purified by anti-FLAG affinity chromatography followed by overnight dialysis and a final gel-filtration. | ||||||||||||||||||||||||||||||
Specimen support |
| ||||||||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: 3 uL sample/grid blotted for 12 s before plunge-freezing |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal magnification: 97902 X / Calibrated magnification: 35714 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80.15 K |
Image recording | Average exposure time: 0.8 sec. / Electron dose: 2.1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 2720 |
EM imaging optics | Energyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 371671 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60556 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|