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Yorodumi- EMDB-6499: Structural insights into the regulatory mechanism of ATM kinase a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6499 | |||||||||
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Title | Structural insights into the regulatory mechanism of ATM kinase activation | |||||||||
Map data | Reconstruction of monomeric ATM kinase | |||||||||
Sample |
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Keywords | DNA-damage response / ataxia telangiectasia / PIKK | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Lau WCY / Li Y / Liu Z / Gao Y / Zhang Q / Huen MSY | |||||||||
Citation | Journal: Cell Cycle / Year: 2016 Title: Structure of the human dimeric ATM kinase. Authors: Wilson C Y Lau / Yinyin Li / Zhe Liu / Yuanzhu Gao / Qinfen Zhang / Michael S Y Huen / Abstract: DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves ...DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6499.map.gz | 582.9 KB | EMDB map data format | |
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Header (meta data) | emd-6499-v30.xml emd-6499.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 400_6499.gif 80_6499.gif | 26.5 KB 2.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6499 | HTTPS FTP |
-Validation report
Summary document | emd_6499_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_6499_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_6499_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6499 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6499.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of monomeric ATM kinase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.61 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Monomeric ATM kinase
Entire | Name: Monomeric ATM kinase |
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Components |
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-Supramolecule #1000: Monomeric ATM kinase
Supramolecule | Name: Monomeric ATM kinase / type: sample / ID: 1000 / Details: The sample was mono disperse / Oligomeric state: Monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 350 KDa |
-Macromolecule #1: Monomeric ATM kinase
Macromolecule | Name: Monomeric ATM kinase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 350 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293T / Recombinant plasmid: pcDNA-FLAG-His-ATM wt |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 8 / Details: 25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol |
Staining | Type: NEGATIVE / Details: 1% w/v uranyl acetate |
Grid | Details: Continuous carbon coated copper grids |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2010 |
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Temperature | Average: 296 K |
Date | Jul 1, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 251 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: class average |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: PRIME, EMAN2 / Number images used: 6546 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | Residues 2021-2118 are removed |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient |