6L54: SMG189

Structure of SMG189. Determined by electron microscopy at 3.43 Å resolution. Released 15 Apr 2020.

Method
Electron microscopy
Resolution
3.43 Å
Organism
Homo sapiens
Chains
3
Atoms
19,530
Mol. weight
579.06 kDa
Ligands
GTP, MG
Released
15 Apr 2020

Explore 6L54 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L54 contains 148 α-helices and 28 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: 119 helices, 9 β-strands

ElementResiduesLengthSheet
α-helix38-425
α-helix62-698
α-helix70-734
α-helix81-888
α-helix97-1026
α-helix103-1053
α-helix114-1174
α-helix124-14118
α-helix151-1533
α-helix154-1629
α-helix171-1744
α-helix178-1814
α-helix189-19810
α-helix202-2043
α-helix211-22212
α-helix230-24516
α-helix251-26818
α-helix279-29214
α-helix301-31212
α-helix322-3243
α-helix326-3305
α-helix339-35517
α-helix363-3664
α-helix380-3878
α-helix389-3946
α-helix399-41921
α-helix421-4244
α-helix426-4283
α-helix445-45511
α-helix456-4594
α-helix473-4797
α-helix481-4844
α-helix488-4914
α-helix494-50815
α-helix545-55713
α-helix563-58018
α-helix598-6003
α-helix606-61611
α-helix625-6306
α-helix642-65211
α-helix659-6679
α-helix715-72511
α-helix735-74511
α-helix764-7674
α-helix809-82315
α-helix834-84916
α-helix869-88921
α-helix905-9084
α-helix909-9124
α-helix916-9216
α-helix925-9306
α-helix935-94713
α-helix973-98412
α-helix989-99810
α-helix1011-10155
α-helix1017-10204
α-helix1027-10337
α-helix1074-10774
α-helix1078-10803
α-helix1081-10844
α-helix1093-110311
α-helix1118-11214
α-helix1124-11318
α-helix1196-12049
α-helix1206-12149
α-helix1283-129614
α-helix1298-13014
α-helix1302-13043
α-helix1316-133015
α-helix1351-13555
α-helix1356-136712
α-helix1400-141011
α-helix1417-142711
α-helix1454-146512
α-helix1467-147913
α-helix1486-149914
α-helix1512-15165
α-helix1524-153310
α-helix1534-15385
α-helix1589-15935
α-helix1599-16079
α-helix1618-163922
α-helix1645-165410
α-helix1661-167616
α-helix1701-171212
α-helix1728-173811
α-helix1740-175920
α-helix1785-179814
α-helix1804-18107
α-helix1824-18263
α-helix1838-185013
α-helix1853-18553
α-helix1861-18644
α-helix1927-193812
α-helix1942-195817
α-helix1965-19706
α-helix1976-199015
α-helix2011-20144
α-helix2015-202713
α-helix20401
α-helix2041-20455
α-helix2049-20524
α-helix2072-208312
α-helix2098-21014
β-strand2128-212921
β-strand2139-214021
β-strand2153-215422
α-helix2162-217817
α-helix2190-21923
β-strand2195-219622
β-strand2204-220522
β-strand2212-221323
α-helix2214-223017
α-helix2251-22555
α-helix2280-22889
α-helix2295-23028
α-helix2307-233024
β-strand234114
β-strand2342-234323
β-strand235214
α-helix2361-23633
α-helix2378-23814
α-helix2392-240514
α-helix2408-241811
α-helix3609-362012
α-helix3633-364311
α-helix3647-36515
α-helix3655-36573
Chain B: 19 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix7-104
β-strand48-5255
α-helix63-719
β-strand139-14355
β-strand148-15255
α-helix161-17010
α-helix182-20524
β-strand209-21135
α-helix222-23615
α-helix238-2425
α-helix252-2576
α-helix2631
β-strand264-26525
β-strand267-27046
α-helix296-31419
β-strand334-33746
α-helix350-36011
α-helix412-42211
α-helix445-45915
α-helix479-4813
α-helix483-4853
α-helix491-50313
α-helix504-5085
α-helix509-5135
α-helix524-53613
α-helix545-55612
Chain C: 10 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand18417
β-strand19017
α-helix195-1973
β-strand205-21068
α-helix219-2257
β-strand259-26028
β-strand265-26958
α-helix276-2849
α-helix297-31317
β-strand317-32158
α-helix328-34013
β-strand36619
β-strand368-37038
β-strand374110
α-helix377-3793
α-helix381-39414
β-strand40119
β-strand423-42428
β-strand427110
α-helix466-47914
α-helix492-50716
α-helix510-5178

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Serine/threonine-protein kinase SMG1Aprotein3661Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG8Bprotein991Homo sapiensQ8ND04 (AlphaFold model)
Protein SMG9Cprotein520Homo sapiensQ9H0W8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6L54_1 Serine/threonine-protein kinase SMG1 (chains A)
MSRRAPGSRLSSGGGGGGTKYPRSWNDWQPRTDSASADPDNLKYSSSRDRGGSSSYGLQP
SNSAVVSRQRHDDTRVHADIQNDEKGGYSVNGGSGENTYGRKSLGQELRVNNVTSPEFTS
VQHGSRALATKDMRKSQERSMSYSDESRLSNLLRRITREDDRDRRLATVKQLKEFIQQPE
NKLVLVKQLDNILAAVHDVLNESSKLLQELRQEGACCLGLLCASLSYEAEKIFKWIFSKF
SSSAKDEVKLLYLCATYKALETVGEKKAFSSVMQLVMTSLQSILENVDTPELLCKCVKCI
LLVARCYPHIFSTNFRDTVDILVGWHIDHTQKPSLTQQVSGWLQSLEPFWVADLAFSTTL
LGQFLEDMEAYAEDLSHVASGESVDEDVPPPSVSLPKLAALLRVFSTVVRSIGERFSPIR
GPPITEAYVTDVLYRVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVIT
YGLDQLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLRYHKEKE
VVAVAHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQLPEACSEIKHEAFKNH
VFNVDNAKFVVIFDLSALTTIGNAKNSLIGMWALSPTVFALLSKNLMIVHSDLAVHFPAI
QYAVLYTLYSHCTRHDHFISSSLSSSSPSLFDGAVISTVTTATKKHFSIILNLLGILLKK
DNLNQDTRKLLMTWALEAAVLMKKSETYAPLFSLPSFHKFCKGLLANTLVEDVNICLQAC
SSLHALSSSLPDDLLQRCVDVCRVQLVHSGTRIRQAFGKLLKSIPLDVVLSNNNHTEIQE
ISLALRSHMSKAPSNTFHPQDFSDVISFILYGNSHRTGKDNWLERLFYSCQRLDKRDQST
IPRNLLKTDAVLWQWAIWEAAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQD
VSQWTTADNDEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTSPPKVIRTFFYTNR
QTCQDWLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTTSLSQGNELEVTIMMVVEAL
CELHCPEAIQGIAVWSSSIVGKNLLWINSVAQQAEGRFEKASVEYQEHLCAMTGVDCCIS
SFDKSVLTLANAGRNSASPKHSLNGESRKTVLSKPTDSSPEVINYLGNKACECYISIADW
AAVQEWQNAIHDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECTEQLELLPGENINLL
AGGSKEKIDMKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALNPIEQDQKWQSITENV
VKYLKQTSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALENTVSNRLSTEDCLIPLFSE
ALRSCKQHDVRPWMQALRYTMYQNQLLEKIKEQTVPIRSHLMELGLTAAKFARKRGNVSL
ATRLLAQCSEVQLGKTTTAQDLVQHFKKLSTQGQVDEKWGPELDIEKTKLLYTAGQSTHA
MEMLSSCAISFCKSVKAEYAVAKSILTLAKWIQAEWKEISGQLKQVYRAQHQQNFTGLST
LSKNILTLIELPSVNTMEEEYPRIESESTVHIGVGEPDFILGQLYHLSSVQAPEVAKSWA
ALASWAYRWGRKVVDNASQGEGVRLLPREKSEVQNLLPDTITEEEKERIYGILGQAVCRP
AGIQDEDITLQITESEDNEEDDMVDVIWRQLISSCPWLSELDESATEGVIKVWRKVVDRI
FSLYKLSCSAYFTFLKLNAGQIPLDEDDPRLHLSHRVEQSTDDMIVMATLRLLRLLVKHA
GELRQYLEHGLETTPTAPWRGIIPQLFSRLNHPEVYVRQSICNLLCRVAQDSPHLILYPA
IVGTISLSSESQASGNKFSTAIPTLLGNIQGEELLVSECEGGSPPASQDSNKDEPKSGLN
EDQAMMQDCYSKIVDKLSSANPTMVLQVQMLVAELRRVTVLWDELWLGVLLQQHMYVLRR
IQQLEDEVKRVQNNNTLRKEEKIAIMREKHTALMKPIVFALEHVRSITAAPAETPHEKWF
QDNYGDAIENALEKLKTPLNPAKPGSSWIPFKEIMLSLQQRAQKRASYILRLEEISPWLA
AMTNTEIALPGEVSARDTVTIHSVGGTITILPTKTKPKKLLFLGSDGKSYPYLFKGLEDL
HLDERIMQFLSIVNTMFATINRQETPRFHARHYSVTPLGTRSGLIQWVDGATPLFGLYKR
WQQREAALQAQKAQDSYQTPQNPGIVPRPSELYYSKIGPALKTVGLSLDVSRRDWPLHVM
KAVLEELMEATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGDRHLDN
VLIDMTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGVTGVEGVFRLSCEQVL
HIMRRGRETLLTLLEAFVYDPLVDWTAGGEAGFAGAVYGGGGQQAESKQSKREMEREITR
SLFSSRVAEIKVNWFKNRDEMLVVLPKLDGSLDEYLSLQEQLTDVEKLQGKLLEEIEFLE
GAEGVDHPSHTLQHRYSEHTQLQTQQRAVQEAIQVKLNEFEQWITHYQAAFNNLEATQLA
SLLQEISTQMDLGPPSYVPATAFLQNAGQAHLISQCEQLEGEVGALLQQRRSVLRGCLEQ
LHHYATVALQYPKAIFQKHRIEQWKTWMEELICNTTVERCQELYRKYEMQYAPQPPPTVC
QFITATEMTLQRYAADINSRLIRQVERLKQEAVTVPVCEDQLKEIERCIKVFLHENGEEG
SLSLASVIISALCTLTRRNLMMEGAASSAGEQLVDLTSRDGAWFLEELCSMSGNVTCLVQ
LLKQCHLVPQDLDIPNPMEASETVHLANGVYTSLQELNSNFRQIIFPEALRCLMKGEYTL
ESMLHELDGLIEQTTDGVPLQTLVESLQAYLRNAAMGLEEETHAHYIDVARLLHAQYGEL
IQPRNGSVDETPKMSAGQMLLVAFDGMFAQVETAFSLLVEKLNKMEIPIAWRKIDIIREA
RSTQVNFFDDDNHRQVLEEIFFLKRLQTIKEFFRLCGTFSKTLSGSSSLEDQNTVNGPVQ
IVNVKTLFRNSCFSEDQMAKPIKAFTADFVRQLLIGLPNQALGLTLCSFISALGVDIIAQ
VEAKDFGAESKVSVDDLCKKAVEHNIQIGKFSQLVMNRATVLASSYDTAWKKHDLVRRLE
TSISSCKTSLQRVQLHIAMFQWQHEDLLINRPQAMSVTPPPRSAILTSMKKKLHTLSQIE
TSIATVQEKLAALESSIEQRLKWAGGANPALAPVLQDFEATIAERRNLVLKESQRASQVT
FLCSNIIHFESLRTRTAEALNLDAALFELIKRCQQMCSFASQFNSSVSELELRLLQRVDT
GLEHPIGSSEWLLSAHKQLTQDMSTQRAIQTEKEQQIETVCETIQNLVDNIKTVLTGHNR
QLGDVKHLLKAMAKDEEAALADGEDVPYENSVRQFLGEYKSWQDNIQTVLFTLVQAMGQV
RSQEHVEMLQEITPTLKELKTQSQSIYNNLVSFASPLVTDATNECSSPTSSATYQPSFAA
AVRSNTGQKTQPDVMSQNARKLIQKNLATSADTPPSTVPGTGKSVACSPKKAVRDPKTGK
AVQERNSYAVSVWKRVKAKLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAW
V
Sequence of entity 2 (B), FASTA
>6L54_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
>6L54_3 Protein SMG9 (chains C)
MSESGHSQPGLYGIERRRRWKEPGSGGPQNLSGPGGRERDYIAPWERERRDASEETSTSV
MQKTPIILSKPPAERSKQPPPPTAPAAPPAPAPLEKPIVLMKPREEGKGPVAVTGASTPE
GTAPPPPAAPAPPKGEKEGQRPTQPVYQIQNRGMGTAAPAAMDPVVGQAKLLPPERMKHS
IKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDQRTYVFRA
QSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRKLPPEYNLPHTYV
EMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPSHESSSSSGSDEG
TEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPD
FLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQSLVSKLRSQVMSM
ARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA

Ligands and cofactors

IDNameFormulaCopies
GTPGuanosine-5'-triphosphateC10 H16 N5 O14 P31
MGMagnesium ionMg1

Primary citation

Cryo-EM structure of SMG1-SMG8-SMG9 complex. Zhu, L., Li, L., Qi, Y. et al. Cell Res (2019) 29:1027-1034. DOI 10.1038/s41422-019-0255-3 · PubMed

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

Browse structure collections

About this viewer

MolViewer shows 6L54 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.