+Open data
-Basic information
Entry | Database: PDB / ID: 6syt | ||||||
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Title | Structure of the SMG1-SMG8-SMG9 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Kinase / NMD / IP6 / G-fold protein / PIKK family | ||||||
Function / homology | Function and homology information diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of protein kinase activity / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus ...diacylglycerol-dependent serine/threonine kinase activity / chromatoid body / eye development / regulation of protein kinase activity / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / brain development / heart development / peptidyl-serine phosphorylation / in utero embryonic development / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
Authors | Gat, Y. / Schuller, J.M. / Conti, E. | ||||||
Funding support | Germany, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6syt.cif.gz | 491 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6syt.ent.gz | 348.9 KB | Display | PDB format |
PDBx/mmJSON format | 6syt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6syt_validation.pdf.gz | 961.8 KB | Display | wwPDB validaton report |
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Full document | 6syt_full_validation.pdf.gz | 971.1 KB | Display | |
Data in XML | 6syt_validation.xml.gz | 63.3 KB | Display | |
Data in CIF | 6syt_validation.cif.gz | 100.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/6syt ftp://data.pdbj.org/pub/pdb/validation_reports/sy/6syt | HTTPS FTP |
-Related structure data
Related structure data | 10347MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 401403.938 Da / Num. of mol.: 1 Mutation: D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Source method: isolated from a genetically manipulated source Details: Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of ...Details: Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R,Inactive D2335A mutant of SMG1. The automatic alignment is wrong. With the numbering here - residues 2486 to the end (from the coordinates) should be aligned with residues 3659 to the end of the sequence. The following residues are modeled as Alanine 147-156 162-175 191-201 207-224 248-265 267-285 290-304 311-312 1646-1657 1663-1677 1703-1717 1962-1965 1967-1978 2006-2021 2068-2083 2248-2265 Residues 1-52 are a tag. our construct has a point mutation compared to the annotated sequence - K743R Source: (gene. exp.) Homo sapiens (human) / Gene: SMG1, SMG1, ATX, KIAA0421, LIP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) References: UniProt: Q96Q15, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 109825.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMG8, ABC2, C17orf71 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8ND04 |
#3: Protein | Mass: 57717.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMG9, C19orf61 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9H0W8 |
-Non-polymers , 3 types, 3 molecules
#4: Chemical | ChemComp-IHP / |
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#5: Chemical | ChemComp-ATP / |
#6: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SMG1-SMG8-SMG9 PIKK Kinase complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK293T |
Buffer solution | pH: 7.5 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 52.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214254 / Symmetry type: POINT |