7PW5: PDB entry 7PW5

Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor. Determined by electron microscopy at 3.4 Å resolution. Released 1 Dec 2021.

Method
Electron microscopy
Resolution
3.4 Å
Organism
Homo sapiens
Chains
3
Atoms
21,548
Mol. weight
566.7 kDa
Ligands
MG, ATP, 88C, IHP
Released
1 Dec 2021

Explore 7PW5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PW5 contains 172 α-helices and 75 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: 118 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix148-1558
α-helix166-1694
α-helix170-1734
α-helix192-1976
α-helix208-21811
α-helix230-24314
α-helix249-26416
α-helix271-28414
α-helix291-30212
α-helix314-3229
α-helix336-34611
α-helix356-37520
α-helix395-41016
α-helix429-44315
α-helix450-46617
α-helix476-48611
α-helix494-51017
α-helix517-5215
α-helix530-5334
α-helix539-55315
α-helix558-58225
α-helix590-5923
α-helix595-5973
α-helix604-61714
α-helix619-6224
α-helix638-6403
α-helix641-6455
α-helix648-6503
α-helix653-6564
α-helix658-67316
α-helix676-6783
α-helix699-7024
α-helix707-71913
α-helix725-74420
α-helix749-7524
α-helix755-76713
α-helix773-78513
α-helix792-80514
β-strand80811
α-helix812-82211
α-helix826-8294
α-helix833-8353
α-helix836-85015
α-helix852-8532
α-helix859-8668
α-helix867-8715
α-helix882-8898
α-helix903-9075
β-strand90811
α-helix909-92618
α-helix936-95520
α-helix970-99829
α-helix1006-10094
α-helix1010-10189
α-helix1020-104021
α-helix1044-105714
α-helix1069-108214
α-helix1086-109611
α-helix1107-11148
α-helix1118-113316
α-helix1144-11507
α-helix1180-119617
α-helix1200-121718
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-helix1418-143417
α-helix1438-144912
α-helix1459-14668
α-helix1480-149314
α-helix1497-151115
α-helix1521-153414
α-helix1540-155011
α-helix1560-156910
α-helix1589-15913
α-helix1596-161116
α-helix1616-163621
α-helix1647-16559
α-helix1664-167310
α-helix1704-171613
α-helix1729-173911
α-helix1743-175614
α-helix1782-179817
α-helix1804-18107
α-helix1823-18286
α-helix1836-184914
α-helix1857-18648
α-helix1925-193713
α-helix1942-195716
α-helix1963-197715
α-helix2007-202014
α-helix2037-20437
α-helix2047-20559
α-helix2069-208214
α-helix21071
β-strand210812
α-helix21091
β-strand212012
β-strand2123-212423
β-strand2129-213024
β-strand2138-214034
β-strand2142-214323
β-strand214913
β-strand2152-215434
α-helix2161-217515
α-helix2180-21834
β-strand2195-219734
β-strand2203-220644
β-strand2212-221325
α-helix2215-223117
α-helix2249-226416
α-helix2277-228812
α-helix2297-23037
α-helix2307-233125
α-helix2338-23403
β-strand2341-234335
β-strand2350-235235
α-helix2362-23643
α-helix2377-23815
α-helix2391-240515
α-helix2407-241812
α-helix3608-362114
α-helix3633-364311
α-helix3647-36504
α-helix3655-36573
Chain B: 38 helices, 46 β-strands
ElementResiduesLengthSheet
β-strand5-626
α-helix8-114
α-helix40-423
β-strand48-5476
β-strand5617
α-helix63-7210
β-strand137-14376
β-strand148-15476
β-strand15817
α-helix159-17113
α-helix182-20322
β-strand209-21356
α-helix222-24423
α-helix253-2575
β-strand264-27076
α-helix296-31419
β-strand32816
β-strand336-33946
α-helix340-3412
α-helix347-35913
α-helix410-42213
α-helix445-45713
α-helix478-4825
α-helix489-50820
α-helix524-53815
α-helix544-55613
β-strand56518
β-strand56919
β-strand57519
β-strand57918
β-strand582110
α-helix583-5853
α-helix588-5903
β-strand591110
β-strand598110
β-strand606-610511
β-strand617-621511
α-helix626-6272
α-helix628-6325
α-helix633-6386
β-strand646-648312
α-helix649-6513
α-helix6601
β-strand661-662213
α-helix663-6642
α-helix740-7423
β-strand745-746213
β-strand747114
β-strand752115
α-helix7561
β-strand761114
β-strand767-772612
α-helix774-7763
β-strand778116
β-strand782116
β-strand788112
α-helix7891
β-strand796-801612
α-helix839-8413
β-strand842-8531212
β-strand855111
β-strand858-863612
β-strand866-867212
α-helix879-8835
α-helix8861
β-strand887-888215
β-strand890-892312
α-helix902-9032
β-strand904-9141112
β-strand919-923517
β-strand927-929315
α-helix935-9362
β-strand937115
β-strand944-946317
α-helix9471
β-strand950-955612
α-helix956-9572
β-strand960-962318
β-strand965-967318
α-helix968-9714
α-helix976-9783
β-strand979-981315
α-helix9821
β-strand986-990517
Chain C: 16 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand181-184419
β-strand190119
α-helix195-1973
β-strand202120
β-strand205-211721
α-helix217-2259
α-helix233-2353
α-helix243-2464
β-strand256-258319
β-strand259-260221
β-strand265-268421
α-helix271-2722
α-helix276-2838
α-helix298-31417
β-strand317-322621
α-helix330-33910
β-strand366-374921
α-helix376-3783
α-helix381-39414
β-strand401121
β-strand403122
α-helix408-4114
α-helix419-4213
β-strand426122
β-strand428-432521
α-helix454-4563
α-helix466-47813
β-strand491120
α-helix492-50716
α-helix511-5177

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase…Aprotein3657Homo sapiensQ96Q15 (AlphaFold model)
Protein SMG8Bprotein991Homo sapiensQ8ND04 (AlphaFold model)
Protein SMG9Cprotein520Homo sapiensQ9H0W8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7PW5_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 (chains A)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Sequence of entity 2 (B), FASTA
>7PW5_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
>7PW5_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
88C1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridi…C27 H28 Cl N7 O3 S1
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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