7PW9: Human SMG1-9 kinase complex

Human SMG1-9 kinase complex bound to AMPPNP. Determined by electron microscopy at 3.12 Å resolution. Released 1 Dec 2021.

Method
Electron microscopy
Resolution
3.12 Å
Organism
Homo sapiens
Chains
2
Atoms
16,339
Mol. weight
439.06 kDa
Ligands
ANP, IHP, ATP, MG
Released
1 Dec 2021

Explore 7PW9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PW9 contains 131 α-helices and 29 β-strands across 2 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: 118 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix148-1558
α-helix166-1749
α-helix192-1987
α-helix208-21811
α-helix230-24314
α-helix249-26416
α-helix271-28414
α-helix291-30212
α-helix315-3228
α-helix336-34611
α-helix356-37520
α-helix395-41016
α-helix430-44314
α-helix450-46617
α-helix475-48713
α-helix494-51017
α-helix517-5237
α-helix529-5335
α-helix539-55315
α-helix558-58124
α-helix595-5973
α-helix604-62219
α-helix638-6403
α-helix641-6455
α-helix648-6503
α-helix653-6564
α-helix658-67417
α-helix676-6783
α-helix699-7035
α-helix707-71812
α-helix725-74117
α-helix746-7538
α-helix755-76713
α-helix773-78513
α-helix792-80514
β-strand80811
α-helix811-82313
α-helix826-8294
α-helix833-8353
α-helix836-85015
α-helix852-8532
α-helix859-87113
α-helix882-8898
α-helix903-9053
β-strand90811
α-helix909-92618
α-helix938-95518
α-helix970-99829
α-helix1006-10094
α-helix1010-10189
α-helix1020-104021
α-helix1044-105714
α-helix1068-108215
α-helix1086-109611
α-helix1106-111510
α-helix1118-113316
α-helix1144-11507
α-helix1180-119617
α-helix1200-121516
α-helix1228-123912
α-helix1243-12497
α-helix1256-12583
α-helix12751
α-helix1282-130423
α-helix1320-133112
α-helix1333-13408
α-helix1348-136619
α-helix1371-13733
α-helix1379-13835
α-helix1391-140616
α-helix1407-14093
α-helix1418-143417
α-helix1438-144912
α-helix1459-14668
α-helix1480-149415
α-helix1497-151216
α-helix1519-153416
α-helix1540-155011
α-helix1560-156910
α-helix1587-15904
α-helix1596-161116
α-helix1616-163621
α-helix1647-16559
α-helix1664-167310
α-helix1704-171512
α-helix1729-174012
α-helix1742-175716
α-helix1782-179817
α-helix1804-18107
α-helix1823-18286
α-helix1829-18313
α-helix1836-184914
α-helix1853-18553
α-helix1858-18647
α-helix1925-193814
α-helix1942-195918
α-helix1962-197716
α-helix2007-201913
α-helix2036-20438
α-helix2047-20559
α-helix2069-208214
β-strand2090-209122
α-helix2092-20954
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-helix2180-21834
β-strand2195-219734
β-strand2203-220644
β-strand2212-221325
α-helix2214-223118
α-helix2246-22483
α-helix2249-226214
α-helix2277-229014
α-helix2295-23039
α-helix2307-233125
α-helix2338-23403
β-strand2341-234335
β-strand2350-235235
α-helix2361-23633
α-helix2377-23815
α-helix2391-240515
α-helix2407-241812
α-helix3608-362114
α-helix3633-364513
α-helix3647-36515
Chain C: 13 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand181-18446
β-strand19016
α-helix195-1973
β-strand20217
β-strand205-21066
α-helix217-2259
α-helix233-2353
α-helix243-2464
β-strand256-26056
β-strand265-27066
α-helix271-2722
α-helix276-2838
α-helix296-31419
β-strand317-32266
α-helix330-3378
β-strand366-37496
α-helix381-39414
β-strand40318
α-helix409-4113
β-strand42618
β-strand428-43256
α-helix466-47813
β-strand48619
β-strand48819
β-strand49117
α-helix492-50716
α-helix511-5188

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein…Aprotein3657Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG9Cprotein352Homo sapiensQ9H0W8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7PW9_1 Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1,Serine/threonine-protein kinase SMG1 (chains A)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Sequence of entity 2 (C), FASTA
>7PW9_2 Protein SMG9 (chains C)
AKLLPPERMKHSIKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMVMSLLSANT
PEEDQRTYVFRAQSAEMKERGGNQTSGIDFFITQERIVFLDTQPILSPSILDHLINNDRK
LPPEYNLPHTYVEMQSLQIAAFLFTVCHVVIVVQDWFTDLSLYRFLQTAEMVKPSTPSPS
HESSSSSGSDEGTEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQLMAHSHLRYKGTLSM
LQCNVFPGLPPDFLDSEVNLFLVPFMDSEAESENPPRAGPGSSPLFSLLPGYRGHPSFQS
LVSKLRSQVMSMARPQLSHTILTEKNWFHYAARIWDGVRKSSALAEYSRLLA

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

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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