6SYT: SMG1-SMG8-SMG9 complex

Structure of the SMG1-SMG8-SMG9 complex. Determined by electron microscopy at 3.45 Å resolution. Released 11 Dec 2019.

Method
Electron microscopy
Resolution
3.45 Å
Organism
Homo sapiens
Chains
3
Atoms
18,369
Mol. weight
570.14 kDa
Ligands
IHP, ATP, MG
Released
11 Dec 2019

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

Secondary structure: helices and β-sheets

6SYT contains 138 α-helices and 40 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: 110 helices, 14 β-strands

ElementResiduesLengthSheet
α-helix148-1558
α-helix163-17412
α-helix192-2009
α-helix208-22316
α-helix231-24313
α-helix249-26416
α-helix270-28415
α-helix291-30313
α-helix312-32312
α-helix336-34611
α-helix356-37318
α-helix395-41117
α-helix429-44416
α-helix450-46415
α-helix475-48814
α-helix496-51015
α-helix517-5248
α-helix529-5335
α-helix539-55214
α-helix562-58019
α-helix581-5833
α-helix604-62219
α-helix638-6403
α-helix641-6455
α-helix647-6504
α-helix653-6564
α-helix658-67215
α-helix676-6783
α-helix707-71812
α-helix725-74218
α-helix746-7483
α-helix750-7523
α-helix755-76713
α-helix773-78614
α-helix792-80514
α-helix817-8237
α-helix836-84914
α-helix852-8532
α-helix859-87012
α-helix884-8907
α-helix909-92618
α-helix936-95520
α-helix972-99827
α-helix1020-104021
α-helix1044-105714
α-helix1069-108012
α-helix1081-10833
α-helix1086-109712
α-helix1107-11148
α-helix1118-113316
α-helix1144-11474
α-helix1148-11503
α-helix1180-119516
α-helix1200-121718
α-helix1228-123710
α-helix1242-12498
α-helix1256-12583
α-helix1282-130423
α-helix1317-133014
α-helix1333-13386
α-helix1349-136416
α-helix1371-13733
α-helix1379-13835
α-helix1392-140514
α-helix1406-14094
α-helix1418-143316
α-helix1438-144811
α-helix1460-14667
α-helix1481-149212
α-helix1497-151216
α-helix1518-153215
α-helix1540-154910
α-helix1560-156910
α-helix1587-15893
α-helix1590-15934
α-helix1596-161015
α-helix1617-163418
α-helix1647-165610
α-helix1664-167512
α-helix1705-171612
α-helix1729-174012
α-helix1742-175615
α-helix1782-179817
α-helix1806-18105
α-helix1819-18213
α-helix1823-18275
α-helix1835-184915
α-helix1857-18648
α-helix1924-193815
α-helix1942-195615
α-helix1963-197715
α-helix2007-201812
α-helix2036-205520
α-helix2071-208212
β-strand2090-209121
β-strand210812
β-strand212012
β-strand212113
β-strand2127-212821
β-strand2129-213024
β-strand2138-214254
β-strand214413
β-strand2150-215454
α-helix2162-217413
α-helix2178-21814
β-strand219514
β-strand2204-220634
β-strand2212-221325
α-helix2215-222915
α-helix2249-226315
α-helix2277-228812
α-helix2297-23004
α-helix2301-23033
α-helix2308-233124
β-strand2341-234335
β-strand2350-235235
α-helix2362-23643
α-helix2377-23804
α-helix2391-240515
α-helix2407-241812
α-helix3610-362112
α-helix3633-364513
α-helix3647-36504
α-helix3655-36573
Chain B: 14 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand616
β-strand4617
β-strand48-5476
α-helix65-717
β-strand137-14376
β-strand148-15476
α-helix159-17113
α-helix184-20421
β-strand209-21466
α-helix223-24119
α-helix243-2453
α-helix253-2575
β-strand264-27076
α-helix296-31520
β-strand32816
β-strand337-33936
α-helix348-35912
α-helix410-42213
β-strand44417
α-helix445-45713
α-helix477-4848
α-helix489-50820
α-helix524-53815
α-helix544-55815
Chain C: 14 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand181-18448
β-strand19018
α-helix195-1973
β-strand20219
β-strand205-210610
α-helix220-2256
α-helix233-2353
α-helix243-2464
β-strand256-25838
β-strand259-260210
β-strand265-268410
α-helix271-2722
α-helix276-2838
α-helix296-31419
β-strand317-322610
α-helix328-33710
β-strand366111
β-strand368-374710
α-helix376-3794
α-helix381-39414
β-strand401111
β-strand403112
β-strand407110
α-helix419-4213
β-strand426112
β-strand428-432510
α-helix466-47813
β-strand49119
α-helix492-50716
α-helix511-5188

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase…Aprotein3712Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG8Bprotein991Homo sapiensQ8ND04 (AlphaFold model)
Protein SMG9Cprotein520Homo sapiensQ9H0W8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6SYT_1 SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1 (chains A)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Sequence of entity 2 (B), FASTA
>6SYT_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
>6SYT_3 Protein SMG9 (chains C)
MSESGHSQPGLYGIERRRRWKEPGSGGPQNLSGPGGRERDYIAPWERERRDASEETSTSV
MQKTPIILSKPPAERSKQPPPPTAPAAPPAPAPLEKPIVLMKPREEGKGPVAVTGASTPE
GTAPPPPAAPAPPKGEKEGQRPTQPVYQIQNRGMGTAAPAAMDPVVGQAKLLPPERMKHS
IKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANTPEEDQRTYVFRA
QSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRKLPPEYNLPHTYV
EMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPSHESSSSSGSDEG
TEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSMLQCNVFPGLPPD
FLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQSLVSKLRSQVMSM
ARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P61
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
MGMagnesium ionMg1

Primary citation

InsP6binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex. Gat, Y., Schuller, J.M., Lingaraju, M. et al. Nat Struct Mol Biol (2019) 26:1089-1093. DOI 10.1038/s41594-019-0342-7 · 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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