+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10348 | |||||||||
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Title | CryoEM structure of the SMG1-SMG8-SMG9 complex | |||||||||
Map data | CryoEM map of the SMG1-SMG8-SMG9 complex more complete | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||
Authors | Gat Y / Schuller JM / Conti E | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: InsP binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex. Authors: Yair Gat / Jan Michael Schuller / Mahesh Lingaraju / Elisabeth Weyher / Fabien Bonneau / Mike Strauss / Peter J Murray / Elena Conti / Abstract: We report the 3.45-Å resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance. ...We report the 3.45-Å resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance. Structural and MS analyses reveal the presence of inositol hexaphosphate (InsP) in the SMG1 kinase. We show that the InsP-binding site is conserved in mammalian target of rapamycin (mTOR) and potentially other PIKK members, and that it is required for optimal in vitro phosphorylation of both SMG1 and mTOR substrates. | |||||||||
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_10348.map.gz | 50.2 MB | EMDB map data format | |
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Header (meta data) | emd-10348-v30.xml emd-10348.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_10348.png | 243.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10348 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10348 | HTTPS FTP |
-Validation report
Summary document | emd_10348_validation.pdf.gz | 253.7 KB | Display | EMDB validaton report |
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Full document | emd_10348_full_validation.pdf.gz | 252.8 KB | Display | |
Data in XML | emd_10348_validation.xml.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10348 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10348 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10348.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of the SMG1-SMG8-SMG9 complex more complete | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : SMG1-SMG8-SMG9 PIKK Kinase complex
Entire | Name: SMG1-SMG8-SMG9 PIKK Kinase complex |
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Components |
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-Supramolecule #1: SMG1-SMG8-SMG9 PIKK Kinase complex
Supramolecule | Name: SMG1-SMG8-SMG9 PIKK Kinase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: PBS |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 52.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148835 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |