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Yorodumi- EMDB-3065: A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3065 | |||||||||
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Title | A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation | |||||||||
Map data | contour level in chimera. Reconstruction of the SMG1-SMG8-SMG9-UPF1 complex in conformation 1 | |||||||||
Sample |
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Keywords | Cryo-electron microscopy / SMG-1 kinase / Phosphoinositide-3-kinase-like kinase / UPF1 substrate recruitment / SMG-8-9 kinase regulation / Nonsense-mediated mRNA decay | |||||||||
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: 17.0 Å | |||||||||
Authors | Deniaud A / Karuppasamy M / Bock T / Masiulis S / Huard K / Garzoni F / Kerschgens K / Hentze MW / Kulozik AE / Beck M ...Deniaud A / Karuppasamy M / Bock T / Masiulis S / Huard K / Garzoni F / Kerschgens K / Hentze MW / Kulozik AE / Beck M / Neu-Yilik G / Schaffitzel C | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2015 Title: A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation. Authors: Aurélien Deniaud / Manikandan Karuppasamy / Thomas Bock / Simonas Masiulis / Karine Huard / Frédéric Garzoni / Kathrin Kerschgens / Matthias W Hentze / Andreas E Kulozik / Martin Beck / ...Authors: Aurélien Deniaud / Manikandan Karuppasamy / Thomas Bock / Simonas Masiulis / Karine Huard / Frédéric Garzoni / Kathrin Kerschgens / Matthias W Hentze / Andreas E Kulozik / Martin Beck / Gabriele Neu-Yilik / Christiane Schaffitzel / Abstract: Mammalian nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that degrades mRNAs containing premature translation termination codons. Phosphorylation of the essential NMD ...Mammalian nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance mechanism that degrades mRNAs containing premature translation termination codons. Phosphorylation of the essential NMD effector UPF1 by the phosphoinositide-3-kinase-like kinase (PIKK) SMG-1 is a key step in NMD and occurs when SMG-1, its two regulatory factors SMG-8 and SMG-9, and UPF1 form a complex at a terminating ribosome. Electron cryo-microscopy of the SMG-1-8-9-UPF1 complex shows the head and arm architecture characteristic of PIKKs and reveals different states of UPF1 docking. UPF1 is recruited to the SMG-1 kinase domain and C-terminal insertion domain, inducing an opening of the head domain that provides access to the active site. SMG-8 and SMG-9 interact with the SMG-1 C-insertion and promote high-affinity UPF1 binding to SMG-1-8-9, as well as decelerated SMG-1 kinase activity and enhanced stringency of phosphorylation site selection. The presence of UPF2 destabilizes the SMG-1-8-9-UPF1 complex leading to substrate release. Our results suggest an intricate molecular network of SMG-8, SMG-9 and the SMG-1 C-insertion domain that governs UPF1 substrate recruitment and phosphorylation by SMG-1 kinase, an event that is central to trigger mRNA decay. | |||||||||
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_3065.map.gz | 14.5 MB | EMDB map data format | |
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Header (meta data) | emd-3065-v30.xml emd-3065.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_13518.png | 948.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3065 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3065 | HTTPS FTP |
-Validation report
Summary document | emd_3065_validation.pdf.gz | 234.4 KB | Display | EMDB validaton report |
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Full document | emd_3065_full_validation.pdf.gz | 233.5 KB | Display | |
Data in XML | emd_3065_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3065 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3065 | HTTPS FTP |
-Related 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_3065.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | contour level in chimera. Reconstruction of the SMG1-SMG8-SMG9-UPF1 complex in conformation 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.86 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 : Complex of four proteins: SMG1, SMG8, SMG9 and UPF1
Entire | Name: Complex of four proteins: SMG1, SMG8, SMG9 and UPF1 |
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Components |
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-Supramolecule #1000: Complex of four proteins: SMG1, SMG8, SMG9 and UPF1
Supramolecule | Name: Complex of four proteins: SMG1, SMG8, SMG9 and UPF1 / type: sample / ID: 1000 Details: The sample is monodisperse, and the elution volume in size exclusion chromatography is consistent with a heterotetramer. Oligomeric state: heterotetramer / Number unique components: 4 |
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Molecular weight | Experimental: 720 KDa / Theoretical: 720 KDa / Method: Size exclusion chromatography |
-Macromolecule #1: SMG-1
Macromolecule | Name: SMG-1 / type: protein_or_peptide / ID: 1 / Name.synonym: Serine/threonine-protein kinase SMG1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 420 KDa / Theoretical: 420 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pLexm |
Sequence | UniProtKB: Serine/threonine-protein kinase SMG1 |
-Macromolecule #2: SMG-8
Macromolecule | Name: SMG-8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 110 KDa / Theoretical: 110 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pLexm |
Sequence | UniProtKB: Nonsense-mediated mRNA decay factor SMG8 |
-Macromolecule #3: SMG-9
Macromolecule | Name: SMG-9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 60 KDa / Theoretical: 60 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pLexm |
Sequence | UniProtKB: Nonsense-mediated mRNA decay factor SMG9 |
-Macromolecule #4: UPF1
Macromolecule | Name: UPF1 / type: protein_or_peptide / ID: 4 / Name.synonym: RENT1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 130 KDa / Theoretical: 130 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf21 / Recombinant plasmid: pFastBBac |
Sequence | UniProtKB: Regulator of nonsense transcripts 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 9 Details: 20 mM Tris pH 9.0, 100 mM KCl, 25 mM glycine, 1 mM DTT and 2 mM biotin |
Grid | Details: copper 300 mesh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 2 second blotting and blot force of 3 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 86 K |
Specialist optics | Energy filter - Name: not used |
Date | Jan 30, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1300 / Average electron dose: 13 e/Å2 / Bits/pixel: 32 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: FEI polara multispecimen holder, nitrogen cooled Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: xmipp / Number images used: 26653 |