7PW8: Human SMG1-8-9 kinase complex

Human SMG1-8-9 kinase complex bound to AMPPNP. Determined by electron microscopy at 2.82 Å resolution. Released 1 Dec 2021.

Method
Electron microscopy
Resolution
2.82 Å
Organism
Homo sapiens
Chains
3
Atoms
18,960
Mol. weight
566.64 kDa
Ligands
MG, ATP, ANP, IHP
Released
1 Dec 2021

Explore 7PW8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PW8 contains 151 α-helices and 41 β-strands across 3 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: 116 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix148-1558
α-helix166-1749
α-helix192-1976
α-helix198-2003
α-helix208-21811
α-helix230-24314
α-helix249-26416
α-helix271-28212
α-helix291-30111
α-helix314-3218
α-helix336-34611
α-helix356-37318
α-helix395-41117
α-helix429-44315
α-helix450-46617
α-helix475-48612
α-helix494-51017
α-helix517-5237
α-helix529-5324
α-helix533-5353
α-helix539-55214
α-helix558-58225
α-helix595-5973
α-helix604-62219
α-helix638-6403
α-helix641-6455
α-helix647-6504
α-helix653-6564
α-helix658-67316
α-helix676-6783
α-helix706-71813
α-helix725-74117
α-helix746-7538
α-helix755-76612
α-helix773-78513
α-helix792-80514
β-strand80811
α-helix811-82111
α-helix826-8294
α-helix836-85015
α-helix852-8532
α-helix859-87012
α-helix882-8898
α-helix903-9053
β-strand90811
α-helix909-92618
α-helix936-95520
α-helix970-99829
α-helix1006-10094
α-helix1010-10189
α-helix1020-104021
α-helix1044-105714
α-helix1068-108215
α-helix1086-109611
α-helix1107-11148
α-helix1118-113316
α-helix1144-11507
α-helix1180-119617
α-helix1200-121516
α-helix1228-123912
α-helix1242-12498
α-helix1256-12583
α-helix1282-130423
α-helix1318-133114
α-helix1333-13408
α-helix1348-136619
α-helix1371-13733
α-helix1379-13824
α-helix1391-140616
α-helix1407-14093
α-helix1418-143316
α-helix1438-144912
α-helix1459-14668
α-helix1480-149415
α-helix1497-151115
α-helix1518-153417
α-helix1536-155015
α-helix1560-156910
α-helix1596-161116
α-helix1616-163621
α-helix1647-16559
α-helix1664-167310
α-helix1704-171512
α-helix1729-174012
α-helix1742-175615
α-helix1782-179817
α-helix1804-181310
α-helix1823-18286
α-helix1829-18313
α-helix1836-184914
α-helix1853-18553
α-helix1857-18648
α-helix1925-193814
α-helix1942-195716
α-helix1963-197715
α-helix2007-201913
α-helix2036-20449
α-helix2047-20548
α-helix2069-208214
β-strand2090-209122
α-helix21071
β-strand210813
α-helix21091
β-strand212013
β-strand2121-212444
β-strand2127-212822
β-strand2129-213024
β-strand2138-214474
β-strand2149-215574
α-helix2161-217515
α-helix2180-21823
β-strand2195-219734
β-strand2203-220644
α-helix2207-22082
β-strand2212-221325
α-helix2215-223117
α-helix2246-22483
α-helix2249-226214
α-helix2277-229014
α-helix2295-23039
α-helix2307-233125
β-strand2341-234335
β-strand2350-235235
α-helix2361-23633
α-helix2377-23815
α-helix2391-240515
α-helix2407-241812
α-helix3608-362013
α-helix3633-364513
α-helix3647-36515
α-helix3655-36573
Chain B: 18 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand5-626
α-helix7-115
α-helix40-423
β-strand4617
β-strand48-5476
β-strand5618
α-helix63-719
β-strand137-14376
β-strand148-15476
β-strand15818
α-helix159-17113
α-helix182-20322
β-strand209-21466
α-helix219-2202
α-helix222-23413
α-helix238-2447
α-helix252-2576
β-strand264-27076
α-helix296-31419
β-strand32816
β-strand336-33946
α-helix340-3412
α-helix347-35812
α-helix410-42213
β-strand44417
α-helix445-45713
α-helix478-4825
α-helix489-50820
α-helix524-53815
α-helix544-55714
Chain C: 17 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand181-18449
β-strand19019
α-helix195-1973
β-strand202110
β-strand205-21179
α-helix217-2259
α-helix233-2353
α-helix239-2424
α-helix243-2475
β-strand256-26059
β-strand265-27069
α-helix271-2722
α-helix276-2838
α-helix296-31419
β-strand317-32269
α-helix330-33910
β-strand366-37499
α-helix376-3794
α-helix381-39414
β-strand40119
β-strand403111
β-strand40719
α-helix419-4213
β-strand426111
β-strand428-43259
α-helix454-4563
α-helix457-4604
α-helix466-47813
β-strand491110
α-helix492-50716
α-helix511-5177

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1Aprotein3657Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG8Bprotein991Homo sapiensQ8ND04 (AlphaFold model)
Protein SMG9Cprotein520Homo sapiensQ9H0W8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7PW8_1 SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1 (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXFSTNFRDTVDILVGWHIDHTQKPSLTQQVSGWLQSLEPFWVADLAFSTTLLGQF
LEDMEAYAEDLSHVASGESVDEDVPPPSVSLPKLAALLRVFSTVVRSIGERFSPIRGPPI
TEAYVTDVLYRVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLD
QLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLRYHKEKEVVAV
AHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQLPEACSEIKHEAFKNHVFNV
DNAKFVVIFDLSALTTIGNAKNSLIGMWALSPTVFALLSKNLMIVHSDLAVHFPAIQYAV
LYTLYSHCTRHDHFISSSLSSSSPSLFDGAVISTVTTATKKHFSIILNLLGILLKKDNLN
QDTRKLLMTWALEAAVLMRKSETYAPLFSLPSFHKFCKGLLANTLVEDVNICLQACSSLH
ALSSSLPDDLLQRCVDVCRVQLVHSGTRIRQAFGKLLKSIPLDVVLSNNNHTEIQEISLA
LRSHMSKAPSNTFHPQDFSDVISFILYGNSHRTGKDNWLERLFYSCQRLDKRDQSTIPRN
LLKTDAVLWQWAIWEAAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDVSQW
TTADNDEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTSPPKVIRTFFYTNRQTCQ
DWLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTTSLSQGNELEVTIMMVVEALCELH
CPEAIQGIAVWSSSIVGKNLLWINSVAQQAEGRFEKASVEYQEHLCAMTGVDCCISSFDK
SVLTLANAGRNSASPKHSLNGESRKTVLSKPTDSSPEVINYLGNKACECYISIADWAAVQ
EWQNSIHDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECTEQLELLPGENINLLAGGS
KEKIDMKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALNPIEQDQKWQSITENVVKYL
KQTSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALENTVSNRLSTEDCLIPLFSEALRS
CKQHDVRPWMQALRYTMYQNQLLEKIKEQTVPIRSHLMELGLTAAKFARKRGNVSLATRL
LAQCSEVQLGKTTTAQDLVQHFKKLSTQGQVDEKWGPELDIEKTKLLYTAGQSTHAMEML
SSCAISFCKSVKAEYAVAKSILTLAKWIQAEWKEISGQLKQVYRAQHQQNFTGLSTLSKN
ILTLIELPSVNTMEEEYPRIESESTVHIGVGEPDFILGQLYHLSSVQAPEVAKSWAALAS
WAYRWGRKVVDNASXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEGVIKVWRKVVDRIFSLY
KLSCSAYFTFLKLNAGQIPLDEDDPRLHLSHRVEQSTDDMIVMATLRLLRLLVKHAGELR
QYLEHGLETTPTAPWRGIIPQLFSRLNHPEVYVRQSICNLLCRVAQDSPHLILYPAIVGT
ISLSSESQASGNKFSTAIPTLLGNIQGEELLVSECEGGSPPASQDSNKDEPKSGLNEDQA
MMQDCYSKIVDKLSSANPTMVLQVQMLVAELRRVTVLWDELWLGVLLQQHMYVLXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPHEKWFQDNY
GDAIENALEKLKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYILRLEEISPWLAAMTN
TEIALPGEVSARDTVTIHSVGGTITILPTKTKPKKLLFLGSDGKSYPYLFKGLEDLHLDE
RIMQFLSIVNTMFATINRQETPRFHARHYSVTPLGTRSGLIQWVDGATPLFGLYKRWQQR
EAALQAQKAQDSYQTPQNPGIVPRPSELYYSKIGPALKTVGLSLDVSRRDWPLHVMKAVL
EELMEATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGDRHLDNVLID
MTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGVTGVEGVFRLSCEQVLHIMR
RGRETLLTLLEAFVYDPLVDWTAGGEAGFAGAVYGGGGQQAESKQSKREMEREITRSLFS
SRVAEIKVNWFKNRDEMLVVLPKLDGSLDEYLSLQEQLTDVEKLQGKLLEEIEFLEGAEG
VDHPSHTLQHRYSEHTQLQTQQRAVQEAIQVKLNEFEQWITHYQAAFNNLEATQLASLLQ
EISTQMDLGPPSYVPATAFLQNAGQAHLISQCEQLEGEVGALLQQRRSVLRGCLEQLHHY
ATVALQYPKAIFQKHRIEQWKTWMEELICNTTVERCQELYRKYEMQYAPQPPPTVCQFIT
ATEMTLQRYAADINSRLIRQVERLKQEAVTVPVCEDQLKEIERCIKVFLHENGEEGSLSL
ASVIISALCTLTRRNLMMEGAASSAGEQLVDLTSRDGAWFLEELCSMSGNVTCLVQLLKQ
CHLVPQDLDIPNPMEASETVHLANGVYTSLQELNSNFRQIIFPEALRCLMKGEYTLESML
HELDGLIEQTTDGVPLQTLVESLQAYLRNAAMGLEEETHAHYIDVARLLHAQYGELIQPR
NGSVDETPKMSAGQMLLVAFDGMFAQVETAFSLLVEKLNKMEIPIAWRKIDIIREARSTQ
VNFFDDDNHRQVLEEIFFLKRLQTIKEFFRLCGTFSKTLSGSSSLEDQNTVNGPVQIVNV
KTLFRNSCFSEDQMAKPIKAFTADFVRQLLIGLPNQALGLTLCSFISALGVDIIAQVEAK
DFGAESKVSVDDLCKKAVEHNIQIGKFSQLVMNRATVLASSYDTAWKKHDLVRRLETSIS
SCKTSLQRVQLHIAMFQWQHEDLLINRPQAMSVTPPPRSAILTSMKKKLHTLSQIETSIA
TVQEKLAALESSIEQRLKWAGGANPALAPVLQDFEATIAERRNLVLKESQRASQVTFLCS
NIIHFESLRTRTAEALNLDAALFELIKRCQQMCSFASQFNSSVSELELRLLQRVDTGLEH
PIGSSEWLLSAHKQLTQDMSTQRAIQTEKEQQIETVCETIQNLVDNIKTVLTGHNRQLGD
VKHLLKAMAKDEEAALADGEDVPYENSVRQFLGEYKSWQDNIQTVLFTLVQAMGQVRSQE
HVEMLQEITPTLKELKTQSQSIYNNLVSFASPLVTDATNECSSPTSSATYQPSFAAAVRS
NTGQKTQPDVMSQNARKLIQKNLATSADTPPSTVPGTGKSVACSPKKAVRDPKTGKAVQE
RNSYAVSVWKRVKAKLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV
Sequence of entity 2 (B), FASTA
>7PW8_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
>7PW8_3 Protein SMG9 (chains C)
MSESGHSQPGLYGIERRRRWKEPGSGGPQNLSGPGGRERDYIAPWERERRDASEETSTSV
MQKTPIILSKPPAERSKQPPPPTAPAAPPAPAPLEKPIVLMKPREEGKGPVAVTGASTPE
GTAPPPPAAPAPPKGEKEGQRPTQPVYQIQNRGMGTAAPAAMDPVVGQAKLLPPERMKHS
IKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDQRTYVFRA
QSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRKLPPEYNLPHTYV
EMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPSHESSSSSGSDEG
TEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPD
FLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQSLVSKLRSQVMSM
ARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA

Ligands and cofactors

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

Primary citation

Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8. Langer, L.M., Bonneau, F., Gat, Y. et al. Elife (2021) 10. DOI 10.7554/eLife.72353 · 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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