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- PDB-6syt: Structure of the SMG1-SMG8-SMG9 complex -

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Entry
Database: PDB / ID: 6syt
TitleStructure of the SMG1-SMG8-SMG9 complex
Components
  • Protein SMG8
  • Protein SMG9
  • SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
KeywordsSIGNALING PROTEIN / Kinase / NMD / IP6 / G-fold protein / PIKK family
Function / homology
Function and homology information


regulation of protein kinase activity / diacylglycerol-dependent serine/threonine kinase activity / eye development / chromatoid body / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...regulation of protein kinase activity / diacylglycerol-dependent serine/threonine kinase activity / eye development / chromatoid body / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / phosphatidylinositol phosphate biosynthetic process / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / brain development / heart development / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / peptidyl-serine phosphorylation / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / protein autophosphorylation / in utero embryonic development / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine/threonine kinase activity / protein serine kinase activity / DNA repair / DNA damage response / negative regulation of apoptotic process / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / : ...Nonsense-mediated mRNA decay factor SMG8/SMG9 / Smg8_Smg9 / Nonsense-mediated mRNA decay factor SMG9 / Serine/threonine-protein kinase SMG1 / Serine/threonine-protein kinase SMG1, N-terminal / SMG1, PIKK catalytic domain / Serine/threonine-protein kinase smg-1 / Serine/threonine-protein kinase SMG1 N-terminal / Rapamycin binding domain / : / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Nonsense-mediated mRNA decay factor SMG8 / Serine/threonine-protein kinase SMG1 / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsGat, Y. / Schuller, J.M. / Conti, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: 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
DepositionOct 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 7, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
B: Protein SMG8
C: Protein SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,1396
Polymers568,9473
Non-polymers1,1923
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11750 Å2
ΔGint-93 kcal/mol
Surface area112870 Å2
MethodPISA

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1 / hSMG-1 / 61E3.4 / Lambda/iota protein kinase C-interacting protein / Lambda-interacting 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
#2: Protein Protein SMG8 / Amplified in breast cancer gene 2 protein / Protein smg-8 homolog


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 Protein SMG9 / Protein SMG-9


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

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SMG1-SMG8-SMG9 PIKK Kinase complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293T
Buffer solutionpH: 7.5 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 52.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214254 / Symmetry type: POINT

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