+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4095 | |||||||||
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Title | Negative stain EM-structure of Checkpoint point kinase Tel1 | |||||||||
Map data | Negative stain structure of dimeric Tel1. | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.7 Å | |||||||||
Authors | Darbari VC / Sawicka M / Wanrooij PH / Hailemariam S / Zhang X / Burgers PM | |||||||||
Citation | Journal: J Biol Chem / Year: 2016 Title: The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization. Authors: Marta Sawicka / Paulina H Wanrooij / Vidya C Darbari / Elias Tannous / Sarem Hailemariam / Daniel Bose / Alena V Makarova / Peter M Burgers / Xiaodong Zhang / Abstract: The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play ...The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signaling, and repair. Here, we present the first structural insight for dimers of Mec1·Ddc2 and Tel1 using single-particle electron microscopy. Both kinases reveal a head to head dimer with one major dimeric interface through the N-terminal HEAT (named after Huntingtin, elongation factor 3, protein phosphatase 2A, and yeast kinase TOR1) repeat. Their dimeric interface is significantly distinct from the interface of mTOR complex 1 dimer, which oligomerizes through two spatially separate interfaces. We also observe different structural organizations of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1·Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated, providing potential access of substrates to this kinase, even in its dimeric form. | |||||||||
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_4095.map.gz | 315.9 KB | EMDB map data format | |
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Header (meta data) | emd-4095-v30.xml emd-4095.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4095_fsc.xml | 4.3 KB | Display | FSC data file |
Images | emd_4095.png | 59.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4095 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4095 | HTTPS FTP |
-Validation report
Summary document | emd_4095_validation.pdf.gz | 218.9 KB | Display | EMDB validaton report |
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Full document | emd_4095_full_validation.pdf.gz | 218.1 KB | Display | |
Data in XML | emd_4095_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4095 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4095 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4095.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain structure of dimeric Tel1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.64 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 : Tel1 protein
Entire | Name: Tel1 protein |
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Components |
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-Supramolecule #1: Tel1 protein
Supramolecule | Name: Tel1 protein / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: BJ2168 / Recombinant plasmid: pBL602 |
Molecular weight | Theoretical: 640 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: 2% Uranyl Acetate | ||||||||||||||||||||||||||||||
Grid | Model: TAAB / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 38000 |