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- EMDB-0837: SMG189 -

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Basic information

Entry
Database: EMDB / ID: EMD-0837
TitleSMG189
Map data
Sample
  • Organelle or cellular component: SMG189 complex
    • Protein or peptide: Serine/threonine-protein kinase SMG1
    • Protein or peptide: Protein SMG8
    • Protein or peptide: Protein SMG9
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsSMG189 / Cryo-EM / Nonsense-mediated mRNA decay / TRANSFERASE-TRANSCRIPTION complex
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
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 ...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
Nonsense-mediated mRNA decay factor SMG8 / Serine/threonine-protein kinase SMG1 / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsXu Y / Qi Y
CitationJournal: Cell Res / Year: 2019
Title: Cryo-EM structure of SMG1-SMG8-SMG9 complex.
Authors: Li Zhu / Liang Li / Yilun Qi / Zishuo Yu / Yanhui Xu /
Abstract: Nonsense-mediated mRNA decay (NMD) targets premature stop codon (PTC)-containing mRNAs for rapid degradation, and is essential for mammalian embryonic development, brain development and modulation of ...Nonsense-mediated mRNA decay (NMD) targets premature stop codon (PTC)-containing mRNAs for rapid degradation, and is essential for mammalian embryonic development, brain development and modulation of the stress response. The key event in NMD is the SMG1-mediated phosphorylation of an RNA helicase UPF1 and SMG1 kinase activity is inhibited by SMG8 and SMG9 in an unknown mechanism. Here, we determined the cryo-EM structures of human SMG1 at 3.6 Å resolution and the SMG1-SMG8-SMG9 complex at 3.4 Å resolution, respectively. SMG8 has a C-terminal kinase inhibitory domain (KID), which covers the catalytic pocket and inhibits the kinase activity of SMG1. Structural analyses suggest that GTP hydrolysis of SMG9 would lead to a dramatic conformational change of SMG8-SMG9 and the KID would move away from the inhibitory position to restore SMG1 kinase activity. Thus, our structural and biochemical analyses provide a mechanistic understanding of SMG1-SMG8-SMG9 complex assembly and the regulatory mechanism of SMG1 kinase activity.
History
DepositionOct 22, 2019-
Header (metadata) releaseApr 15, 2020-
Map releaseApr 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l54
  • Surface level: 7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0837.png

Downloads & links

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Map

FileDownload / File: emd_0837.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 6.5 / Movie #1: 6.5
Minimum - Maximum-23.750622 - 48.493175999999998
Average (Standard dev.)-0.000000000001397 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-23.75148.493-0.000

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Supplemental data

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Sample components

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Entire : SMG189 complex

EntireName: SMG189 complex
Components
  • Organelle or cellular component: SMG189 complex
    • Protein or peptide: Serine/threonine-protein kinase SMG1
    • Protein or peptide: Protein SMG8
    • Protein or peptide: Protein SMG9
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SMG189 complex

SupramoleculeName: SMG189 complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase SMG1

MacromoleculeName: Serine/threonine-protein kinase SMG1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 410.966969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSRRAPGSRL SSGGGGGGTK YPRSWNDWQP RTDSASADPD NLKYSSSRDR GGSSSYGLQP SNSAVVSRQR HDDTRVHADI QNDEKGGYS VNGGSGENTY GRKSLGQELR VNNVTSPEFT SVQHGSRALA TKDMRKSQER SMSYSDESRL SNLLRRITRE D DRDRRLAT ...String:
MSRRAPGSRL SSGGGGGGTK YPRSWNDWQP RTDSASADPD NLKYSSSRDR GGSSSYGLQP SNSAVVSRQR HDDTRVHADI QNDEKGGYS VNGGSGENTY GRKSLGQELR VNNVTSPEFT SVQHGSRALA TKDMRKSQER SMSYSDESRL SNLLRRITRE D DRDRRLAT VKQLKEFIQQ PENKLVLVKQ LDNILAAVHD VLNESSKLLQ ELRQEGACCL GLLCASLSYE AEKIFKWIFS KF SSSAKDE VKLLYLCATY KALETVGEKK AFSSVMQLVM TSLQSILENV DTPELLCKCV KCILLVARCY PHIFSTNFRD TVD ILVGWH IDHTQKPSLT QQVSGWLQSL EPFWVADLAF STTLLGQFLE DMEAYAEDLS HVASGESVDE DVPPPSVSLP KLAA LLRVF STVVRSIGER FSPIRGPPIT EAYVTDVLYR VMRCVTAANQ VFFSEAVLTA ANECVGVLLG SLDPSMTIHC DMVIT YGLD QLENCQTCGT DYIISVLNLL TLIVEQINTK LPSSFVEKLF IPSSKLLFLR YHKEKEVVAV AHAVYQAVLS LKNIPV LET AYKLILGEMT CALNNLLHSL QLPEACSEIK HEAFKNHVFN VDNAKFVVIF DLSALTTIGN AKNSLIGMWA LSPTVFA LL SKNLMIVHSD LAVHFPAIQY AVLYTLYSHC TRHDHFISSS LSSSSPSLFD GAVISTVTTA TKKHFSIILN LLGILLKK D NLNQDTRKLL MTWALEAAVL MKKSETYAPL FSLPSFHKFC KGLLANTLVE DVNICLQACS SLHALSSSLP DDLLQRCVD VCRVQLVHSG TRIRQAFGKL LKSIPLDVVL SNNNHTEIQE ISLALRSHMS KAPSNTFHPQ DFSDVISFIL YGNSHRTGKD NWLERLFYS CQRLDKRDQS TIPRNLLKTD AVLWQWAIWE AAQFTVLSKL RTPLGRAQDT FQTIEGIIRS LAAHTLNPDQ D VSQWTTAD NDEGHGNNQL RLVLLLQYLE NLEKLMYNAY EGCANALTSP PKVIRTFFYT NRQTCQDWLT RIRLSIMRVG LL AGQPAVT VRHGFDLLTE MKTTSLSQGN ELEVTIMMVV EALCELHCPE AIQGIAVWSS SIVGKNLLWI NSVAQQAEGR FEK ASVEYQ EHLCAMTGVD CCISSFDKSV LTLANAGRNS ASPKHSLNGE SRKTVLSKPT DSSPEVINYL GNKACECYIS IADW AAVQE WQNAIHDLKK STSSTSLNLK ADFNYIKSLS SFESGKFVEC TEQLELLPGE NINLLAGGSK EKIDMKKLLP NMLSP DPRE LQKSIEVQLL RSSVCLATAL NPIEQDQKWQ SITENVVKYL KQTSRIAIGP LRLSTLTVSQ SLPVLSTLQL YCSSAL ENT VSNRLSTEDC LIPLFSEALR SCKQHDVRPW MQALRYTMYQ NQLLEKIKEQ TVPIRSHLME LGLTAAKFAR KRGNVSL AT RLLAQCSEVQ LGKTTTAQDL VQHFKKLSTQ GQVDEKWGPE LDIEKTKLLY TAGQSTHAME MLSSCAISFC KSVKAEYA V AKSILTLAKW IQAEWKEISG QLKQVYRAQH QQNFTGLSTL SKNILTLIEL PSVNTMEEEY PRIESESTVH IGVGEPDFI LGQLYHLSSV QAPEVAKSWA ALASWAYRWG RKVVDNASQG EGVRLLPREK SEVQNLLPDT ITEEEKERIY GILGQAVCRP AGIQDEDIT LQITESEDNE EDDMVDVIWR QLISSCPWLS ELDESATEGV IKVWRKVVDR IFSLYKLSCS AYFTFLKLNA G QIPLDEDD PRLHLSHRVE QSTDDMIVMA TLRLLRLLVK HAGELRQYLE HGLETTPTAP WRGIIPQLFS RLNHPEVYVR QS ICNLLCR VAQDSPHLIL YPAIVGTISL SSESQASGNK FSTAIPTLLG NIQGEELLVS ECEGGSPPAS QDSNKDEPKS GLN EDQAMM QDCYSKIVDK LSSANPTMVL QVQMLVAELR RVTVLWDELW LGVLLQQHMY VLRRIQQLED EVKRVQNNNT LRKE EKIAI MREKHTALMK PIVFALEHVR SITAAPAETP HEKWFQDNYG DAIENALEKL KTPLNPAKPG SSWIPFKEIM LSLQQ RAQK RASYILRLEE ISPWLAAMTN TEIALPGEVS ARDTVTIHSV GGTITILPTK TKPKKLLFLG SDGKSYPYLF KGLEDL HLD ERIMQFLSIV NTMFATINRQ ETPRFHARHY SVTPLGTRSG LIQWVDGATP LFGLYKRWQQ REAALQAQKA QDSYQTP QN PGIVPRPSEL YYSKIGPALK TVGLSLDVSR RDWPLHVMKA VLEELMEATP PNLLAKELWS SCTTPDEWWR VTQSYARS T AVMSMVGYII GLGDRHLDNV LIDMTTGEVV HIDYNVCFEK GKSLRVPEKV PFRMTQNIET ALGVTGVEGV FRLSCEQVL HIMRRGRETL LTLLEAFVYD PLVDWTAGGE AGFAGAVYGG GGQQAESKQS KREMEREITR SLFSSRVAEI KVNWFKNRDE MLVVLPKLD GSLDEYLSLQ EQLTDVEKLQ GKLLEEIEFL EGAEGVDHPS HTLQHRYSEH TQLQTQQRAV QEAIQVKLNE F EQWITHYQ AAFNNLEATQ LASLLQEIST QMDLGPPSYV PATAFLQNAG QAHLISQCEQ LEGEVGALLQ QRRSVLRGCL EQ LHHYATV ALQYPKAIFQ KHRIEQWKTW MEELICNTTV ERCQELYRKY EMQYAPQPPP TVCQFITATE MTLQRYAADI NSR LIRQVE RLKQEAVTVP VCEDQLKEIE RCIKVFLHEN GEEGSLSLAS VIISALCTLT RRNLMMEGAA SSAGEQLVDL TSRD GAWFL EELCSMSGNV TCLVQLLKQC HLVPQDLDIP NPMEASETVH LANGVYTSLQ ELNSNFRQII FPEALRCLMK GEYTL ESML HELDGLIEQT TDGVPLQTLV ESLQAYLRNA AMGLEEETHA HYIDVARLLH AQYGELIQPR NGSVDETPKM SAGQML LVA FDGMFAQVET AFSLLVEKLN KMEIPIAWRK IDIIREARST QVNFFDDDNH RQVLEEIFFL KRLQTIKEFF RLCGTFS KT LSGSSSLEDQ NTVNGPVQIV NVKTLFRNSC FSEDQMAKPI KAFTADFVRQ LLIGLPNQAL GLTLCSFISA LGVDIIAQ V EAKDFGAESK VSVDDLCKKA VEHNIQIGKF SQLVMNRATV LASSYDTAWK KHDLVRRLET SISSCKTSLQ RVQLHIAMF QWQHEDLLIN RPQAMSVTPP PRSAILTSMK KKLHTLSQIE TSIATVQEKL AALESSIEQR LKWAGGANPA LAPVLQDFEA TIAERRNLV LKESQRASQV TFLCSNIIHF ESLRTRTAEA LNLDAALFEL IKRCQQMCSF ASQFNSSVSE LELRLLQRVD T GLEHPIGS SEWLLSAHKQ LTQDMSTQRA IQTEKEQQIE TVCETIQNLV DNIKTVLTGH NRQLGDVKHL LKAMAKDEEA AL ADGEDVP YENSVRQFLG EYKSWQDNIQ TVLFTLVQAM GQVRSQEHVE MLQEITPTLK ELKTQSQSIY NNLVSFASPL VTD ATNECS SPTSSATYQP SFAAAVRSNT GQKTQPDVMS QNARKLIQKN LATSADTPPS TVPGTGKSVA CSPKKAVRDP KTGK AVQER NSYAVSVWKR VKAKLEGRDV DPNRRMSVAE QVDYVIKEAT NLDNLAQLYE GWTAWV

UniProtKB: Serine/threonine-protein kinase SMG1

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Macromolecule #2: Protein SMG8

MacromoleculeName: Protein SMG8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.82575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA ...String:
MAGPVSLRDL LMGASAWMGS ESPGGSPTEG GGSAAGGPEP PWREDEICVV GIFGKTALRL NSEKFSLVNT VCDRQVFPLF RHQDPGDPG PGIRTEAGAV GEAGGAEDPG AAAGGSVRGS GAVAEGNRTE AGSQDYSLLQ AYYSQESKVL YLLLTSICDN S QLLRACRA LQSGEAGGGL SLPHAEAHEF WKHQEKLQCL SLLYLFSVCH ILLLVHPTCS FDITYDRVFR ALDGLRQKVL PL LKTAIKD CPVGKDWKLN CRPCPPRLLF LFQLNGALKV EPPRNQDPAH PDKPKKHSPK RRLQHALEDQ IYRIFRKSRV LTN QSINCL FTVPANQAFV YIVPGSQEED PVGMLLDQLR SHCTVKDPES LLVPAPLSGP RRYQVMRQHS RQQLSFHIDS SSSS SSGQL VDFTLREFLW QHVELVLSKK GFDDSVGRNP QPSHFELPTY QKWISAASKL YEVAIDGKEE DLGSPTGELT SKILS SIKV LEGFLDIDTK FSENRCQKAL PMAHSAYQSN LPHNYTMTVH KNQLAQALRV YSQHARGPAF HKYAMQLHED CYKFWS NGH QLCEERSLTD QHCVHKFHSL PKSGEKPEAD RNPPVLYHNS RARSTGACNC GRKQAPRDDP FDIKAANYDF YQLLEEK CC GKLDHINFPV FEPSTPDPAP AKNESSPAPP DSDADKLKEK EPQTQGESTS LSLALSLGQS TDSLGTYPAD PQAGGDNP E VHGQVEVKTE KRPNFVDRQA STVEYLPGML HSNCPKGLLP KFSSWSLVKL GPAKSYNFHT GLDQQGFIPG TNYLMPWDI VIRTRAEDEG DLDTNSWPAP NKAIPGKRSA VVMGRGRRRD DIARAFVGFE YEDSRGRRFM CSGPDKVMKV MGSGPKESAL KALNSDMPL YILSSSQGRG LKPHYAQLMR LFVVVPDAPL QIILMPQVQP GPPPCPVFYP EKQEITLPPD GLWVLRFPYA Y VTERGPCF PPKENVQLMS YKVLRGVLKA VTQ

UniProtKB: Nonsense-mediated mRNA decay factor SMG8

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Macromolecule #3: Protein SMG9

MacromoleculeName: Protein SMG9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.717473 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ ...String:
MSESGHSQPG LYGIERRRRW KEPGSGGPQN LSGPGGRERD YIAPWERERR DASEETSTSV MQKTPIILSK PPAERSKQPP PPTAPAAPP APAPLEKPIV LMKPREEGKG PVAVTGASTP EGTAPPPPAA PAPPKGEKEG QRPTQPVYQI QNRGMGTAAP A AMDPVVGQ AKLLPPERMK HSIKLVDDQM NWCDSAIEYL LDQTDVLVVG VLGLQGTGKS MVMSLLSANT PEEDQRTYVF RA QSAEMKE RGGNQTSGID FFITQERIVF LDTQPILSPS ILDHLINNDR KLPPEYNLPH TYVEMQSLQI AAFLFTVCHV VIV VQDWFT DLSLYRFLQT AEMVKPSTPS PSHESSSSSG SDEGTEYYPH LVFLQNKARR EDFCPRKLRQ MHLMIDQLMA HSHL RYKGT LSMLQCNVFP GLPPDFLDSE VNLFLVPFMD SEAESENPPR AGPGSSPLFS LLPGYRGHPS FQSLVSKLRS QVMSM ARPQ LSHTILTEKN WFHYAARIWD GVRKSSALAE YSRLLA

UniProtKB: Nonsense-mediated mRNA decay factor SMG9

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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