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- EMDB-11063: Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ -

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Basic information

Entry
Database: EMDB / ID: EMD-11063
TitleStructure of SMG1-8-9 kinase complex bound to UPF1-LSQ
Map dataSMG1-8-9 with bound UPF1-LSQ
Sample
  • Complex: SMG1-8-9 bound to AMPPNP and UPF1-LSQ
    • Complex: SMG1-8-9
      • Protein or peptide: Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1
      • Protein or peptide: Protein SMG8
      • Protein or peptide: Protein SMG9
    • Complex: UPF1-LSQ
      • Protein or peptide: Regulator of nonsense transcripts 1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCryo-EM / Structural Biology / Nonsense-mediated mRNA decay / RNA quality control / PIKK / NMD / Substrate / Phosphorylation / TRANSFERASE
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / regulation of protein kinase activity / cell cycle phase transition / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / diacylglycerol-dependent serine/threonine kinase activity / regulation of translational termination ...positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / regulation of protein kinase activity / cell cycle phase transition / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / diacylglycerol-dependent serine/threonine kinase activity / regulation of translational termination / histone mRNA catabolic process / chromatoid body / 3'-UTR-mediated mRNA destabilization / eye development / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of telomere maintenance / 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) / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / P-body / helicase activity / brain development / peptidyl-serine phosphorylation / heart development / protein autophosphorylation / cellular response to lipopolysaccharide / in utero embryonic development / DNA helicase / chromosome, telomeric region / DNA replication / RNA helicase activity / non-specific serine/threonine protein kinase / protein kinase activity / RNA helicase / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / chromatin binding / negative regulation of apoptotic process / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-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 ...RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-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 / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / Rapamycin binding domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / : / 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 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Armadillo-type fold / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nonsense-mediated mRNA decay factor SMG8 / Regulator of nonsense transcripts 1 / Serine/threonine-protein kinase SMG1 / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLanger LM / Gat Y
CitationJournal: 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
DepositionMay 21, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0312
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0312
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z3r
  • Surface level: 0.0312
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11063.png

Downloads & links

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Map

FileDownload / File: emd_11063.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSMG1-8-9 with bound UPF1-LSQ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0312 / Movie #1: 0.0312
Minimum - Maximum-0.09087175 - 0.22174887
Average (Standard dev.)0.00020539449 (±0.0036891904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 350.71997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0910.2220.000

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Supplemental data

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Sample components

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Entire : SMG1-8-9 bound to AMPPNP and UPF1-LSQ

EntireName: SMG1-8-9 bound to AMPPNP and UPF1-LSQ
Components
  • Complex: SMG1-8-9 bound to AMPPNP and UPF1-LSQ
    • Complex: SMG1-8-9
      • Protein or peptide: Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1
      • Protein or peptide: Protein SMG8
      • Protein or peptide: Protein SMG9
    • Complex: UPF1-LSQ
      • Protein or peptide: Regulator of nonsense transcripts 1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SMG1-8-9 bound to AMPPNP and UPF1-LSQ

SupramoleculeName: SMG1-8-9 bound to AMPPNP and UPF1-LSQ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 577 KDa

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Supramolecule #2: SMG1-8-9

SupramoleculeName: SMG1-8-9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: UPF1-LSQ

SupramoleculeName: UPF1-LSQ / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine/threonine-protein kinase SMG1,Serine/threonine-protein kin...

MacromoleculeName: Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,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: 379.584781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)ALETVGE KKAFSSVMQL VMTSLQSILE NVDTPELLCK CVKCILLVAR CYPHIFST N FRDTVDILVG WHIDHTQKPS LTQQVSGWLQ SLEPFWVADL AFSTTLLGQF LEDMEAYAED LSHVASGESV DEDVPPPSV SLPKLAALLR VFSTVVRSIG ERFSPIRGPP ITEAYVTDVL YRVMRCVTAA NQVFFSEAVL TAANECVGVL LGSLDPSMTI HCDMVITYG LDQLENCQTC GTDYIISVLN LLTLIVEQIN TKLPSSFVEK LFIPSSKLLF LRYHKEKEVV AVAHAVYQAV L SLKNIPVL ETAYKLILGE MTCALNNLLH SLQLPEACSE IKHEAFKNHV FNVDNAKFVV IFDLSALTTI GNAKNSLIGM WA LSPTVFA LLSKNLMIVH SDLAVHFPAI QYAVLYTLYS HCTRHDHFIS SSLSSSSPSL FDGAVISTVT TATKKHFSII LNL LGILLK KDNLNQDTRK LLMTWALEAA VLMRKSETYA PLFSLPSFHK FCKGLLANTL VEDVNICLQA CSSLHALSSS LPDD LLQRC VDVCRVQLVH SGTRIRQAFG KLLKSIPLDV VLSNNKHTEI QEISLALRSH MSKAPSNTFH PQDFSDVISF ILYGN SHRT GKDNWLERLF YSCQRLDKRD QSTIPRNLLK TDAVLWQWAI WEAAQFTVLS KLRTPLGRAQ DTFQTIEGII RSLAAH TLN PDQDVSQWTT ADNDEGHGNN QLRLVLLLQY LENLEKLMYN AYEGCANALT SPPKVIRTFF YTNRQTCQDW LTRIRLS IM RVGLLAGQPA VTVRHGFDLL TEMKTTSLSQ GNELEVTIMM VVEALCELHC PEAIQGIAVW SSSIVGKNLL WINSVAQQ A EGRFEKASVE YQEHLCAMTG VDCCISSFDK SVLTLANAGR NSASPKHSLN GESRKTVLSK PTDSSPEVIN YLGNKACEC YISIADWAAV QEWQNSIHDL KKSTSSTSLN LKADFNYIKS LSSFESGKFV ECTEQLELLP GENINLLAGG SKEKIDMKKL LPNMLSPDP RELQKSIEVQ LLRSSVCLAT ALNPIEQDQK WQSITENVVK YLKQTSRIAI GPLRLSTLTV SQSLPVLSTL Q LYCSSALE NTVSNRLSTE DCLIPLFSEA LRSCKQHDVR PWMQALRYTM YQNQLLEKIK EQTVPIRSHL MELGLTAAKF AR KRGNVSL ATRLLAQCSE VQLGKTTTAQ DLVQHFKKLS TQGQVDEKWG PELDIEKTKL LYTAGQSTHA MEMLSSCAIS FCK SVKAEY AVAKSILTLA KWIQAEWKEI SGQLKQVYRA QHQQNFTGLS TLSKNILTLI ELPSVNTMEE EYPRIESEST VHIG VGEPD FILGQLYHLS SVQAPEVAKS WAALASWAYR WGRKVVDNAS (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)EGVIK VWRKVVDRIF SLYKLSCSAY FTFLKLNAGQ IPLDEDDPRL HLSHRVEQST DDMIVMATLR LLRLLVKHA GELRQYLEHG LETTPTAPWR GIIPQLFSRL NHPEVYVRQS ICNLLCRVAQ DSPHLILYPA IVGTISLSSE S QASGNKFS TAIPTLLGNI QGEELLVSEC EGGSPPASQD SNKDEPKSGL NEDQAMMQDC YSKIVDKLSS ANPTMVLQVQ ML VAELRRV TVLWDELWLG VLLQQHMYVL RRIQQLEDEV KRVQNNNTLR KEEKIAIMRE KHTALMKPIV FALEHVRSIT AAP AETPHE KWFQDNYGDA IENALEKLK(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)YILR LEEISPWLAA MTNTEIALPG EVSARDTVTI HSVGGTITIL PTKTKPKKLL F LGSDGKSY PYLFKGLEDL HLDERIMQFL SIVNTMFATI NRQETPRFHA RHYSVTPLGT RSGLIQWVDG ATPLFGLYKR WQ QREAALQ AQKAQDSYQT PQNPGIVPRP SELYYSKIGP ALKTVGLSLD VSRRDWPLHV MKAVLEELME ATPPNLLAKE LWS SCTTPD EWWRVTQSYA RSTAVMSMVG YIIGLGDRHL DNVLIDMTTG EVVHIDYNVC FEKGKSLRVP EKVPFRMTQN IETA LGVTG VEGVFRLSCE QVLHIMRRGR ETLLTLLEAF VYDPLVDWTA GGEAGFAGAV YGGGGQQAES KQSKREMERE ITRSL FSSR VAEIKVNWFK NRDEMLVVLP KLDGSLDEYL SLQEQLTDVE KLQGKLLEEI EFLEGAEGVD HPSHTLQHRY SEHTQL QTQ QRAVQEAIQV KLNEFEQWIT HYQAAFNNLE ATQLASLLQE ISTQMDLGPP SYVPATAFLQ NAGQAHLISQ CEQLEGE VG ALLQQRRSVL RGCLEQLHHY ATVALQYPKA IFQKHRIEQW KTWMEELICN TTVERCQELY RKYEMQYAPQ PPPTVCQF I TATEMTLQRY AADINSRLIR QVERLKQEAV TVPVCEDQLK EIERCIKVFL HENGEEGSLS LASVIISALC TLTRRNLMM EGAASSAGEQ LVDLTSRDGA WFLEELCSMS GNVTCLVQLL KQCHLVPQDL DIPNPMEASE TVHLANGVYT SLQELNSNFR QIIFPEALR CLMKGEYTLE SMLHELDGLI EQTTDGVPLQ TLVESLQAYL RNAAMGLEEE THAHYIDVAR LLHAQYGELI Q PRNGSVDE TPKMSAGQML LVAFDGMFAQ VETAFSLLVE KLNKMEIPIA WRKIDIIREA RSTQVNFFDD DNHRQVLEEI FF LKRLQTI KEFFRLCGTF SKTLSGSSSL EDQNTVNGPV QIVNVKTLFR NSCFSEDQMA KPIKAFTADF VRQLLIGLPN QAL GLTLCS FISALGVDII AQVEAKDFGA ESKVSVDDLC KKAVEHNIQI GKFSQLVMNR ATVLASSYDT AWKKHDLVRR LETS ISSCK TSLQRVQLHI AMFQWQHEDL LINRPQAMSV TPPPRSAILT SMKKKLHTLS QIETSIATVQ EKLAALESSI EQRLK WAGG ANPALAPVLQ DFEATIAERR NLVLKESQRA SQVTFLCSNI IHFESLRTRT AEALNLDAAL FELIKRCQQM CSFASQ FNS SVSELELRLL QRVDTGLEHP IGSSEWLLSA HKQLTQDMST QRAIQTEKEQ QIETVCETIQ NLVDNIKTVL TGHNRQL GD VKHLLKAMAK DEEAALADGE DVPYENSVRQ FLGEYKSWQD NIQTVLFTLV QAMGQVRSQE HVEMLQEITP TLKELKTQ S QSIYNNLVSF ASPLVTDATN ECSSPTSSAT YQPSFAAAVR SNTGQKTQPD VMSQNARKLI QKNLATSADT PPSTVPGTG KSVACSPKKA VRDPKTGKAV QERNSYAVSV WKRVKAKLEG RDVDPNRRMS VAEQVDYVIK EATNLDNLAQ LYEGWTAWV

UniProtKB: Serine/threonine-protein kinase SMG1, Serine/threonine-protein kinase SMG1, 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: Regulator of nonsense transcripts 1

MacromoleculeName: Regulator of nonsense transcripts 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.236286 KDa
SequenceString:
QPELSQDSYL G

UniProtKB: Regulator of nonsense transcripts 1

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #6: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / 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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4368586
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 481754
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6syt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6z3r:
Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ

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