+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11063 | |||||||||
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Title | Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ | |||||||||
Map data | SMG1-8-9 with bound UPF1-LSQ | |||||||||
Sample |
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Keywords | Cryo-EM / Structural Biology / Nonsense-mediated mRNA decay / RNA quality control / PIKK / NMD / Substrate / Phosphorylation / TRANSFERASE | |||||||||
Function / homology | Function and homology information double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / regulation of translational termination ...double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / regulation of translational termination / histone mRNA catabolic process / eye development / 3'-UTR-mediated mRNA destabilization / regulation of protein kinase activity / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / DNA duplex unwinding / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / helicase activity / P-body / brain development / heart development / peptidyl-serine phosphorylation / chromosome, telomeric region / DNA replication / cellular response to lipopolysaccharide / DNA helicase / protein autophosphorylation / in utero embryonic development / RNA helicase activity / non-specific serine/threonine protein kinase / protein kinase activity / RNA helicase / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / DNA damage response / chromatin / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Langer LM / Gat Y | |||||||||
Citation | Journal: Elife / Year: 2020 Title: Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity. Authors: Lukas M Langer / Yair Gat / Fabien Bonneau / Elena Conti / Abstract: PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of ...PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of an RNA quality control pathway, termed nonsense-mediated mRNA decay (NMD), by phosphorylating the NMD factor UPF1. Phosphorylation of UPF1 occurs in its unstructured N- and C-terminal regions at Serine/Threonine-Glutamine (SQ) motifs. How SMG1 and other PIKKs specifically recognize SQ motifs has remained unclear. Here, we present a cryo-electron microscopy (cryo-EM) reconstruction of a human SMG1-8-9 kinase complex bound to a UPF1 phosphorylation site at an overall resolution of 2.9 Å. This structure provides the first snapshot of a human PIKK with a substrate-bound active site. Together with biochemical assays, it rationalizes how SMG1 and perhaps other PIKKs specifically phosphorylate Ser/Thr-containing motifs with a glutamine residue at position +1 and a hydrophobic residue at position -1, thus elucidating the molecular basis for phosphorylation site recognition. | |||||||||
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_11063.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-11063-v30.xml emd-11063.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11063_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_11063.png | 86.9 KB | ||
Filedesc metadata | emd-11063.cif.gz | 9.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11063 | HTTPS FTP |
-Validation report
Summary document | emd_11063_validation.pdf.gz | 243.7 KB | Display | EMDB validaton report |
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Full document | emd_11063_full_validation.pdf.gz | 242.8 KB | Display | |
Data in XML | emd_11063_validation.xml.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11063 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11063 | HTTPS FTP |
-Related structure data
Related structure data | 6z3rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11063.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SMG1-8-9 with bound UPF1-LSQ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 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 : SMG1-8-9 bound to AMPPNP and UPF1-LSQ
+Supramolecule #1: SMG1-8-9 bound to AMPPNP and UPF1-LSQ
+Supramolecule #2: SMG1-8-9
+Supramolecule #3: UPF1-LSQ
+Macromolecule #1: Serine/threonine-protein kinase SMG1,Serine/threonine-protein kin...
+Macromolecule #2: Protein SMG8
+Macromolecule #3: Protein SMG9
+Macromolecule #4: Regulator of nonsense transcripts 1
+Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #6: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #8: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6293 / Average exposure time: 5.5 sec. / Average electron dose: 68.75 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |