6Z3R: SMG1-8-9 kinase complex

Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ. Determined by electron microscopy at 2.97 Å resolution. Released 24 Jun 2020.

Method
Electron microscopy
Resolution
2.97 Å
Organism
Homo sapiens
Chains
4
Atoms
18,987
Mol. weight
550.06 kDa
Ligands
ANP, IHP, ATP, MG
Released
24 Jun 2020

Explore 6Z3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z3R contains 146 α-helices and 38 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 112 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix148-1536
α-helix166-1749
α-helix192-1976
α-helix208-21811
α-helix230-24213
α-helix250-26314
α-helix271-28212
α-helix291-30010
α-helix301-3033
α-helix314-3218
α-helix336-34611
α-helix356-37520
α-helix395-41117
α-helix429-44315
α-helix450-46516
α-helix476-48611
α-helix496-51015
α-helix517-5237
α-helix539-55315
α-helix559-58224
α-helix595-5973
α-helix604-62219
α-helix638-6403
α-helix641-6455
α-helix653-6564
α-helix658-67316
α-helix699-7024
α-helix707-71812
α-helix727-74216
α-helix746-7483
α-helix750-7523
α-helix755-76713
α-helix773-78513
α-helix792-80514
α-helix812-82211
α-helix826-8294
α-helix833-8353
α-helix836-85015
α-helix852-8532
α-helix859-87012
α-helix882-8898
α-helix909-92618
α-helix936-95520
α-helix972-99827
α-helix1010-10167
α-helix1020-104021
α-helix1044-105714
α-helix1070-108213
α-helix1086-109712
α-helix1107-11148
α-helix1118-113215
α-helix1144-11485
α-helix1180-119617
α-helix1200-121516
α-helix1228-123912
α-helix1242-12498
α-helix1256-12583
α-helix1282-130423
α-helix1320-133011
α-helix1333-13408
α-helix1349-136416
α-helix1371-13733
α-helix1379-13824
α-helix1391-140616
α-helix1407-14093
α-helix1418-143316
α-helix1438-144912
α-helix1459-14668
α-helix1480-149213
α-helix1497-151115
α-helix1521-153212
α-helix1542-15498
α-helix1560-156910
α-helix1587-15904
α-helix1598-161013
α-helix1617-163519
α-helix1647-16559
α-helix1664-167310
α-helix1704-171613
α-helix1729-174012
α-helix1742-175514
α-helix1782-179817
α-helix1804-18107
α-helix1817-18193
α-helix1823-18286
α-helix1836-184914
α-helix1853-18553
α-helix1857-18648
α-helix1925-193814
α-helix1942-195615
α-helix1963-197715
α-helix2007-201913
α-helix2037-20448
α-helix2047-20548
α-helix2069-208214
β-strand2090-209121
α-helix21071
β-strand210812
α-helix21091
β-strand212012
β-strand2121-212443
β-strand2127-212821
β-strand2129-213024
β-strand2138-213924
β-strand2141-214443
β-strand2150-215123
β-strand2152-215545
α-helix2163-217412
α-helix2175-21773
α-helix2180-21823
β-strand2195-219625
β-strand2203-220645
β-strand2212-221326
α-helix2215-223117
α-helix2249-226315
α-helix2277-228812
α-helix2294-230310
α-helix2307-233125
β-strand2341-234336
β-strand2350-235236
α-helix2377-23804
α-helix2391-240515
α-helix2407-241812
α-helix3608-362114
α-helix3633-364513
α-helix3647-36504
α-helix3655-36573
Chain B: 18 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand5-627
α-helix8-114
α-helix40-423
β-strand48-5477
α-helix65-717
β-strand137-14377
β-strand148-15477
α-helix160-17112
α-helix184-20320
β-strand209-21467
α-helix223-2264
α-helix228-2369
α-helix238-2458
α-helix253-2575
β-strand264-27077
α-helix296-31419
β-strand32817
β-strand336-33947
α-helix347-35711
α-helix410-42213
α-helix437-4393
α-helix445-45612
α-helix478-4825
α-helix489-50820
α-helix524-53815
α-helix544-55714
Chain C: 15 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand181-18448
β-strand19018
α-helix195-1973
β-strand20219
β-strand205-210610
α-helix217-2259
α-helix243-2464
β-strand256-25838
β-strand259-260210
β-strand265-267310
β-strand27018
α-helix271-2722
α-helix276-2838
α-helix296-31419
β-strand317-322610
α-helix330-3378
β-strand366-374910
α-helix376-3783
α-helix381-39414
β-strand401110
β-strand403111
α-helix408-4114
α-helix419-4213
β-strand426111
β-strand428-432510
α-helix454-4563
α-helix466-47712
β-strand49119
α-helix494-50714
α-helix511-5177
Chain E: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix22-232

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase…Aprotein3411Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG8Bprotein991Homo sapiensQ8ND04 (AlphaFold model)
Protein SMG9Cprotein520Homo sapiensQ9H0W8 (AlphaFold model)
Regulator of nonsense transcripts 1Eprotein11Homo sapiensQ92900 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6Z3R_1 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 (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXALETVGEKKAFSSVMQLVMTSLQSILENVDTPELLCKCVKCILLVARCYPH
IFSTNFRDTVDILVGWHIDHTQKPSLTQQVSGWLQSLEPFWVADLAFSTTLLGQFLEDME
AYAEDLSHVASGESVDEDVPPPSVSLPKLAALLRVFSTVVRSIGERFSPIRGPPITEAYV
TDVLYRVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLDQLENC
QTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLRYHKEKEVVAVAHAVY
QAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQLPEACSEIKHEAFKNHVFNVDNAKF
VVIFDLSALTTIGNAKNSLIGMWALSPTVFALLSKNLMIVHSDLAVHFPAIQYAVLYTLY
SHCTRHDHFISSSLSSSSPSLFDGAVISTVTTATKKHFSIILNLLGILLKKDNLNQDTRK
LLMTWALEAAVLMRKSETYAPLFSLPSFHKFCKGLLANTLVEDVNICLQACSSLHALSSS
LPDDLLQRCVDVCRVQLVHSGTRIRQAFGKLLKSIPLDVVLSNNKHTEIQEISLALRSHM
SKAPSNTFHPQDFSDVISFILYGNSHRTGKDNWLERLFYSCQRLDKRDQSTIPRNLLKTD
AVLWQWAIWEAAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDVSQWTTADN
DEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTSPPKVIRTFFYTNRQTCQDWLTR
IRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTTSLSQGNELEVTIMMVVEALCELHCPEAI
QGIAVWSSSIVGKNLLWINSVAQQAEGRFEKASVEYQEHLCAMTGVDCCISSFDKSVLTL
ANAGRNSASPKHSLNGESRKTVLSKPTDSSPEVINYLGNKACECYISIADWAAVQEWQNS
IHDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECTEQLELLPGENINLLAGGSKEKID
MKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALNPIEQDQKWQSITENVVKYLKQTSR
IAIGPLRLSTLTVSQSLPVLSTLQLYCSSALENTVSNRLSTEDCLIPLFSEALRSCKQHD
VRPWMQALRYTMYQNQLLEKIKEQTVPIRSHLMELGLTAAKFARKRGNVSLATRLLAQCS
EVQLGKTTTAQDLVQHFKKLSTQGQVDEKWGPELDIEKTKLLYTAGQSTHAMEMLSSCAI
SFCKSVKAEYAVAKSILTLAKWIQAEWKEISGQLKQVYRAQHQQNFTGLSTLSKNILTLI
ELPSVNTMEEEYPRIESESTVHIGVGEPDFILGQLYHLSSVQAPEVAKSWAALASWAYRW
GRKVVDNASXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEGVIKVWRK
VVDRIFSLYKLSCSAYFTFLKLNAGQIPLDEDDPRLHLSHRVEQSTDDMIVMATLRLLRL
LVKHAGELRQYLEHGLETTPTAPWRGIIPQLFSRLNHPEVYVRQSICNLLCRVAQDSPHL
ILYPAIVGTISLSSESQASGNKFSTAIPTLLGNIQGEELLVSECEGGSPPASQDSNKDEP
KSGLNEDQAMMQDCYSKIVDKLSSANPTMVLQVQMLVAELRRVTVLWDELWLGVLLQQHM
YVLRRIQQLEDEVKRVQNNNTLRKEEKIAIMREKHTALMKPIVFALEHVRSITAAPAETP
HEKWFQDNYGDAIENALEKLKXXXXXXXXXXXXXXXXYILRLEEISPWLAAMTNTEIALP
GEVSARDTVTIHSVGGTITILPTKTKPKKLLFLGSDGKSYPYLFKGLEDLHLDERIMQFL
SIVNTMFATINRQETPRFHARHYSVTPLGTRSGLIQWVDGATPLFGLYKRWQQREAALQA
QKAQDSYQTPQNPGIVPRPSELYYSKIGPALKTVGLSLDVSRRDWPLHVMKAVLEELMEA
TPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGDRHLDNVLIDMTTGEV
VHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGVTGVEGVFRLSCEQVLHIMRRGRETL
LTLLEAFVYDPLVDWTAGGEAGFAGAVYGGGGQQAESKQSKREMEREITRSLFSSRVAEI
KVNWFKNRDEMLVVLPKLDGSLDEYLSLQEQLTDVEKLQGKLLEEIEFLEGAEGVDHPSH
TLQHRYSEHTQLQTQQRAVQEAIQVKLNEFEQWITHYQAAFNNLEATQLASLLQEISTQM
DLGPPSYVPATAFLQNAGQAHLISQCEQLEGEVGALLQQRRSVLRGCLEQLHHYATVALQ
YPKAIFQKHRIEQWKTWMEELICNTTVERCQELYRKYEMQYAPQPPPTVCQFITATEMTL
QRYAADINSRLIRQVERLKQEAVTVPVCEDQLKEIERCIKVFLHENGEEGSLSLASVIIS
ALCTLTRRNLMMEGAASSAGEQLVDLTSRDGAWFLEELCSMSGNVTCLVQLLKQCHLVPQ
DLDIPNPMEASETVHLANGVYTSLQELNSNFRQIIFPEALRCLMKGEYTLESMLHELDGL
IEQTTDGVPLQTLVESLQAYLRNAAMGLEEETHAHYIDVARLLHAQYGELIQPRNGSVDE
TPKMSAGQMLLVAFDGMFAQVETAFSLLVEKLNKMEIPIAWRKIDIIREARSTQVNFFDD
DNHRQVLEEIFFLKRLQTIKEFFRLCGTFSKTLSGSSSLEDQNTVNGPVQIVNVKTLFRN
SCFSEDQMAKPIKAFTADFVRQLLIGLPNQALGLTLCSFISALGVDIIAQVEAKDFGAES
KVSVDDLCKKAVEHNIQIGKFSQLVMNRATVLASSYDTAWKKHDLVRRLETSISSCKTSL
QRVQLHIAMFQWQHEDLLINRPQAMSVTPPPRSAILTSMKKKLHTLSQIETSIATVQEKL
AALESSIEQRLKWAGGANPALAPVLQDFEATIAERRNLVLKESQRASQVTFLCSNIIHFE
SLRTRTAEALNLDAALFELIKRCQQMCSFASQFNSSVSELELRLLQRVDTGLEHPIGSSE
WLLSAHKQLTQDMSTQRAIQTEKEQQIETVCETIQNLVDNIKTVLTGHNRQLGDVKHLLK
AMAKDEEAALADGEDVPYENSVRQFLGEYKSWQDNIQTVLFTLVQAMGQVRSQEHVEMLQ
EITPTLKELKTQSQSIYNNLVSFASPLVTDATNECSSPTSSATYQPSFAAAVRSNTGQKT
QPDVMSQNARKLIQKNLATSADTPPSTVPGTGKSVACSPKKAVRDPKTGKAVQERNSYAV
SVWKRVKAKLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV
Sequence of entity 2 (B), FASTA
>6Z3R_2 Protein SMG8 (chains B)
MAGPVSLRDLLMGASAWMGSESPGGSPTEGGGSAAGGPEPPWREDEICVVGIFGKTALRL
NSEKFSLVNTVCDRQVFPLFRHQDPGDPGPGIRTEAGAVGEAGGAEDPGAAAGGSVRGSG
AVAEGNRTEAGSQDYSLLQAYYSQESKVLYLLLTSICDNSQLLRACRALQSGEAGGGLSL
PHAEAHEFWKHQEKLQCLSLLYLFSVCHILLLVHPTCSFDITYDRVFRALDGLRQKVLPL
LKTAIKDCPVGKDWKLNCRPCPPRLLFLFQLNGALKVEPPRNQDPAHPDKPKKHSPKRRL
QHALEDQIYRIFRKSRVLTNQSINCLFTVPANQAFVYIVPGSQEEDPVGMLLDQLRSHCT
VKDPESLLVPAPLSGPRRYQVMRQHSRQQLSFHIDSSSSSSSGQLVDFTLREFLWQHVEL
VLSKKGFDDSVGRNPQPSHFELPTYQKWISAASKLYEVAIDGKEEDLGSPTGELTSKILS
SIKVLEGFLDIDTKFSENRCQKALPMAHSAYQSNLPHNYTMTVHKNQLAQALRVYSQHAR
GPAFHKYAMQLHEDCYKFWSNGHQLCEERSLTDQHCVHKFHSLPKSGEKPEADRNPPVLY
HNSRARSTGACNCGRKQAPRDDPFDIKAANYDFYQLLEEKCCGKLDHINFPVFEPSTPDP
APAKNESSPAPPDSDADKLKEKEPQTQGESTSLSLALSLGQSTDSLGTYPADPQAGGDNP
EVHGQVEVKTEKRPNFVDRQASTVEYLPGMLHSNCPKGLLPKFSSWSLVKLGPAKSYNFH
TGLDQQGFIPGTNYLMPWDIVIRTRAEDEGDLDTNSWPAPNKAIPGKRSAVVMGRGRRRD
DIARAFVGFEYEDSRGRRFMCSGPDKVMKVMGSGPKESALKALNSDMPLYILSSSQGRGL
KPHYAQLMRLFVVVPDAPLQIILMPQVQPGPPPCPVFYPEKQEITLPPDGLWVLRFPYAY
VTERGPCFPPKENVQLMSYKVLRGVLKAVTQ
Sequence of entity 3 (C), FASTA
>6Z3R_3 Protein SMG9 (chains C)
MSESGHSQPGLYGIERRRRWKEPGSGGPQNLSGPGGRERDYIAPWERERRDASEETSTSV
MQKTPIILSKPPAERSKQPPPPTAPAAPPAPAPLEKPIVLMKPREEGKGPVAVTGASTPE
GTAPPPPAAPAPPKGEKEGQRPTQPVYQIQNRGMGTAAPAAMDPVVGQAKLLPPERMKHS
IKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDQRTYVFRA
QSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRKLPPEYNLPHTYV
EMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPSHESSSSSGSDEG
TEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPD
FLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQSLVSKLRSQVMSM
ARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA
Sequence of entity 4 (E), FASTA
>6Z3R_4 Regulator of nonsense transcripts 1 (chains E)
QPELSQDSYLG

Ligands and cofactors

IDNameFormulaCopies
ANPPhosphoaminophosphonic acid-adenylate esterC10 H17 N6 O12 P31
IHPInositol hexakisphosphateC6 H18 O24 P61
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
MGMagnesium ionMg1

Primary citation

Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity. Langer, L.M., Gat, Y., Bonneau, F. et al. Elife (2020) 9. DOI 10.7554/eLife.57127 · PubMed

Other PDB entries of the same protein (UniProt Q96Q15 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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