9I1J: E3 ubiquitin-protein ligase RNF213

Cryo-EM structure of mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized, and ATPgS. Determined by electron microscopy at 3.8 Å resolution. Released 10 Dec 2025.

Method
Electron microscopy
Resolution
3.8 Å
Organisms
Mus musculus, Homo sapiens
Chains
2
Atoms
36,793
Mol. weight
573.34 kDa
Ligands
ADP, ZN, MG, ATP
Released
10 Dec 2025

Explore 9I1J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I1J contains 251 α-helices and 90 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: 244 helices, 81 β-strands

ElementResiduesLengthSheet
α-helix505-5128
α-helix518-53417
α-helix558-57417
α-helix579-5813
α-helix591-60313
α-helix612-6187
α-helix629-6357
α-helix636-6394
α-helix643-65513
α-helix664-6663
α-helix668-6736
α-helix689-6935
α-helix701-7044
α-helix712-7198
α-helix721-7233
α-helix729-7379
α-helix740-7489
α-helix751-7566
α-helix760-77415
α-helix782-80019
α-helix803-8064
α-helix811-82616
α-helix836-85015
α-helix852-8543
α-helix865-88824
α-helix909-9146
α-helix930-9389
α-helix943-9508
α-helix963-98119
α-helix995-100915
α-helix1022-10309
α-helix1032-104312
α-helix1055-107420
β-strand107911
α-helix1080-10889
α-helix1090-110011
α-helix1114-114330
β-strand114912
α-helix1155-11584
β-strand116611
α-helix1167-11704
β-strand117213
β-strand118213
α-helix1191-120212
α-helix1207-121711
α-helix1218-12203
β-strand123112
α-helix1234-12374
α-helix1238-12425
α-helix1243-125816
α-helix1263-12697
α-helix1270-12723
α-helix1277-129014
α-helix1299-132931
α-helix1339-13468
α-helix1361-13633
α-helix1364-13674
α-helix1368-13703
α-helix1378-13869
α-helix1388-139710
α-helix1404-141411
α-helix1419-144022
α-helix1448-146215
α-helix1468-14769
α-helix1479-14835
α-helix1498-15069
β-strand1508-151144
β-strand1526-153054
β-strand1541-154444
α-helix1545-155612
α-helix1564-159330
β-strand1602-160654
β-strand1612-161654
β-strand1625-162734
α-helix1631-166030
α-helix1668-167811
α-helix1685-16917
α-helix1700-17078
α-helix1713-173018
α-helix1736-174914
α-helix1761-177414
β-strand1793-179645
α-helix1802-18109
β-strand1824-182635
α-helix1833-184311
β-strand1853-185755
α-helix1859-18613
α-helix1864-188017
β-strand1887-189265
α-helix1900-19034
β-strand190915
α-helix1918-192912
α-helix1939-19413
β-strand1949-195356
α-helix1960-197314
β-strand1984-198746
α-helix1994-20018
α-helix2002-20043
β-strand201517
β-strand2017-202046
α-helix2028-20325
α-helix2033-20375
β-strand2040-204238
β-strand2048-205038
β-strand205617
β-strand2058-206256
α-helix2081-20844
β-strand2090-209236
α-helix2096-20994
α-helix2117-21215
α-helix2123-213614
α-helix2155-216410
α-helix2173-219220
α-helix2195-22028
α-helix2208-222316
β-strand2266-226949
β-strand2276-227949
β-strand2282-2285410
β-strand2291-2294410
β-strand2302110
α-helix2309-231810
α-helix2326-23283
α-helix2331-234111
α-helix2358-237316
β-strand2377-2379311
β-strand2380112
α-helix2388-239912
β-strand2407-2411511
α-helix2418-243922
β-strand2444-2448511
α-helix2456-24649
β-strand2467-2468213
β-strand2471-2472213
β-strand2480-2484511
β-strand2490114
α-helix2491-24922
α-helix2493-25008
β-strand2504115
β-strand2516116
β-strand2521116
β-strand2525114
α-helix2529-25335
α-helix2537-25393
β-strand2542112
α-helix2551-256212
α-helix2565-25673
α-helix2572-258817
α-helix2601-261414
α-helix2619-263012
α-helix2633-26353
α-helix2637-26404
α-helix2641-265010
α-helix2651-26555
α-helix2661-26688
α-helix2669-26713
α-helix2674-26763
α-helix2679-269618
α-helix2698-26992
α-helix2707-272115
β-strand2726117
β-strand2729118
α-helix2737-274610
α-helix2755-27584
α-helix27611
β-strand2762-2767617
α-helix2776-279015
β-strand2798-2803617
α-helix2823-28253
β-strand2841-2843317
β-strand2848115
α-helix2853-28553
β-strand2859117
β-strand2862118
α-helix2863-28664
α-helix2868-287811
α-helix2884-28874
α-helix2893-290614
α-helix2914-293118
α-helix2937-294711
α-helix2956-29638
α-helix2965-29673
α-helix2975-29839
α-helix2999-30013
β-strand3002-3006519
α-helix3011-30144
α-helix3015-30195
α-helix3024-30252
β-strand3026-3028319
α-helix3038-305518
β-strand3059-3061319
α-helix3072-30765
β-strand3086-3092720
β-strand3095-3101720
β-strand3107-3112619
α-helix3113-31197
α-helix3123-31275
β-strand3129119
β-strand3132119
α-helix3141-315818
β-strand3160121
α-helix3173-31764
β-strand3177122
α-helix3184-319613
α-helix3205-321814
β-strand3221122
α-helix3223-32286
α-helix3229-32313
β-strand3232121
α-helix3237-32448
α-helix3245-32495
α-helix3255-32639
β-strand3273-3279723
α-helix3282-32843
α-helix3287-32959
β-strand3304-3307423
α-helix3308-33103
α-helix3314-332613
β-strand3334-3339623
α-helix3350-336415
β-strand3372-3378723
β-strand3398-3400323
α-helix3414-34196
α-helix3423-34264
α-helix3477-349014
β-strand3492-3493224
α-helix3502-35109
α-helix3518-353922
α-helix3549-35557
α-helix3557-35626
α-helix3566-358924
α-helix3595-35995
α-helix3605-361511
β-strand3639-3640224
α-helix3658-367518
α-helix3681-369111
α-helix3693-36986
α-helix3703-372119
α-helix3728-374518
α-helix3754-37563
α-helix3761-378424
α-helix3787-379913
α-helix3808-382316
α-helix3829-38379
α-helix3840-38467
α-helix3857-387923
α-helix3880-38845
α-helix3885-38895
α-helix3895-390814
α-helix3918-393922
β-strand3958-3959225
β-strand3965-3966225
α-helix3968-39747
α-helix4001-402626
α-helix4036-40449
β-strand4047126
β-strand4064126
α-helix4083-40886
α-helix4093-40953
α-helix4097-411014
α-helix4117-413822
α-helix4143-415513
α-helix4161-41644
α-helix4172-419625
α-helix4205-421814
α-helix4223-423513
α-helix4238-42447
α-helix4252-42543
α-helix4272-42754
α-helix4280-429213
α-helix4297-43048
α-helix4310-433021
α-helix4332-43343
α-helix4343-435210
α-helix4359-436911
α-helix4386-440217
α-helix4406-44083
α-helix4409-44168
α-helix4418-44214
α-helix4523-454321
α-helix4545-45517
α-helix4560-457718
α-helix4582-459514
α-helix4614-463219
α-helix4639-46479
α-helix4656-46594
α-helix4673-46753
α-helix4692-470110
α-helix4709-47168
α-helix4718-47214
α-helix4724-47263
α-helix4727-474014
β-strand4751127
α-helix4752-47576
α-helix4762-478221
α-helix4786-47894
β-strand4808127
α-helix4821-484121
α-helix4842-48465
β-strand4852-4853228
α-helix4855-48573
α-helix4868-48725
α-helix4873-48775
β-strand4880-4884529
β-strand4890-4894529
α-helix4896-49038
α-helix4904-49085
β-strand4913-4914228
α-helix4916-49183
α-helix4931-494010
α-helix4945-49473
α-helix4948-495710
α-helix4961-497919
α-helix4989-49913
α-helix4992-49965
α-helix5004-50107
α-helix5015-50173
α-helix5018-503518
α-helix5046-50483
α-helix5051-50533
α-helix5054-506512
α-helix5069-508315
α-helix5099-51079
α-helix5116-51194
α-helix5132-514312
α-helix5144-51485
Chain B: 7 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix1-1717
β-strand22-28730
β-strand31-39930
β-strand50131
β-strand51-56630
α-helix65-662
β-strand67-70430
β-strand79132
β-strand84130
β-strand85132
α-helix101-11313
α-helix123-1319
α-helix133-14715
α-helix1481
β-strand149131
α-helix150-1512

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase RNF213Aprotein4836Mus musculusE9Q555
Ubiquitin-conjugating enzyme E2 L3Bprotein166Homo sapiensP68036 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9I1J_1 E3 ubiquitin-protein ligase RNF213 (chains A)
MASWSHPQFEKGSTSAFNPRDTVTVYFHAIVSRHFGFNPEEHKVYVRGGEGLGQKGWTDA
CEMYCTQDLHDLGSLVEGKMDIPRQSLDKPIPYKYVIHRGGSSKDTVEYEFIYEQAQKKG
EHVNRCLRVVSTSLGNGDWHQYDDIICMRSTGFFQQAKNRILDSTRKELLKGKKQAAVVM
LDRIFSVLQPWSDINLQSFMTQFLQFYSVVREPMIHDGRARKWTSLQYEEKEVWTNLWEH
VKKQMAPFLEGKSGESLPADCPVRSKLTLGLSILFMVEAAEFTVPKKDLDSLCYLLIPSA
GSPEALHSDLSPVLRIRQRWRIYLTNLCLRCIDERCDRWLGILPLLHTCMQKSPPKKNSK
SQPEDTWAGLEGISFSEFRDKAPTRSQPLQFMQSKMALLRVDEYLFRSWLSVVPLESLSS
YLENSIDYLSDVPVRVLDCLQGISYRLPGLRKISNQNMKKDVENVFKMLMHLVDIYQHRI
FGENLLQIYLTECLTLHETVCNITANHQFFEIPALSAELICKLLELSPPGHTDEGLPEKS
YEDLVTSTLQEALATTRNWLRSLFKSRMLSISSAYVRLTYSEEMAVWRRLVEIGFPEKHG
WKGSLLGDMEGRLKQEPPRLQISFFCSSQCRDGGLHDSVSRSFEKCVIEAVSSACQSQTS
VLEGLSCQDLQKFGTLLSAVITKSWPVHNGEPVFDVDEIFKYLLKWPDVRQLFELCGTNE
KIIDNITEEGRQLMATAESVFQKVAGELENGTIVVGQLELILEHQSQFLDIWNLNRRRLP
SQEKACDVRSLLKRRRDDLLFLKQEKRYVESLLRQLGRVKHLVQVDFGNIEIIHSQDLSN
KKLNEAVIKLPNSSSYKRETHYCLSPDIREMASKLDSLKDSHIFQDFWQETAESLNTLDK
DPRELKVSLPEVLEYLYNPCYDNFYTLYENLKSGKITFAEVDAIFKDFVDKYDELKNDLK
FMCTMNPQDQKGWISERVGQIKEYHTLHQAVSSAKVILQVRRALGVTGDFSVLNPLLNFA
DSFEDFGNEKLDQISPQFIKAKQLLQDISEPRQRCLEELARQTELVAWLHKALEDINELK
VFVDLASISAGENDIDVDRVACFHDAVQGYASLLYKMDERTNFSDFMNHLQELWRALDND
QHLPDKLKDSARNLEWLKTVKESHGSVELSSLSLATAINSRGVYVIEAPKDGQKISPDTV
LRLLLPDGHGYPEALRTYSTEELKELLNKLMLMSGKKDHNSNTEVEKFSEVFSNMQRLVH
VFIKLHCAGNMLFRTWTAKVYCCPDGGIFMNFGLELLSQLTEKGDVIQLLGALCRQMEDF
LDNWKTVVAQKRAEHFYLNFYTAEQLVYLSSELRKPRPSEAALMMLSFIKGKCTVQDLVQ
ATSACESKADRYCLREVMKKLPQQLLSEPSLMGKLQVIMMQSLVYMSAFLPHCLDLDALG
RCLAHLATMGGTPVERPLPKGLQAGQPNLILCGHSEVLPAALAIYMQAPRQPLPTFDEVL
LCTPATTIEEVELLLRRCLTSGSQGHKVYSLLFADQLSYEVGCQAEEFFQSLCTRAHRED
YQLVILCDAAREHCYIPSTFSQYKVPLVPQAPLPNIQAYLQSHYQVPKRLLSAATVFRDG
LCVGIVTSERAGVGKSLYVNTLHTKLKAKLRDETVPLKIIRLTEPHLDENQVLSALLPFL
KEKYQKMPVIFHIDISTSVQTGIPIFLFKLLILQYLMDINGKIWRRSPGHLYLVEIPQGL
SVQPKRSSKLNARAPLFKFLDLFPKVTCRPPKEVIDMELTPERSHTDPAMDPVEFCSEAF
QRPYQYLKRFHQQQNLDTFQYEKGSVEGSPEECLQHFLIYCGLINPSWSELRNFAWFLNC
QLKDCEASIFCKSAFTGDTLRGFKNFVVTFMILMARDFATPTLHTSDQSPGRQSVTIGEV
VEEDLAPFSLRKRWESEPHPYVFFNGDHMTMTFIGFHLETNNNGYVDAINPSNGKVIKKD
VMTKELFDGLRLQRVPFNIDFDNLPRYEKLERLCLALGIEWPIDPDETYELTTDNMLKIL
AIEMRFRCGIPVIIMGETGCGKTRLIKFLSDLKRGSVEAETMKLVKVHGGTTPSMIYSKV
KEAERTAFSNKAQHKLDTILFFDEANTTEAVSCIKEILCDRTVDGEHLHEDSGLHIIAAC
NPYRKHSQEMILRLESAGLGYRVSAEETADRLGSIPLRQLVYRVHALPPSLIPLVWDFGQ
LNDSAEKLYIQQIVQRLVDSVSVNPSETCVIADVLSASQMFMRKRENECGFVSLRDVERC
VKVFRWFHDHSDMLLKELDKFLHESSDSTHTFERDPVLWSLVMAIGVCYHASLEEKASYR
TAIARCFPKPYNSSRAILDEVTHVQDLFLRGAPIRTNIARNLALKENVFMMVICIELKIP
LFLVGKPGSSKSLAKIIVADAMQGQAAFSELFRCLKQVHLVSFQCSPHSTPQGIISTFKQ
CARFQQGKDLGQYVSVVVLDEVGLAEDSPKMPLKTLHPLLEDGCIEDDPAPYKKVGFVGI
SNWALDPAKMNRGIFVSRGSPNEKELIESAEGICSSDRLVQDKIRGYFAPFAKAYETVCQ
KQDKEFFGLRDYYSLIKMVFAKAKASKRGLSPQDITHAVLRNFSGKDNIQALSIFTASLP
EARYKEEVSTVELIKQNIYPGPQASSRGLDGAESRYLLVLTRNYVALQILQQTFFEGQQP
EIIFGSSFPQDQEYTQICRNINRVKICMETGKMVVLLNLQNLYESLYDALNQYYVYLGGQ
KYVDLGLGTHRVKCRVHTAFRLIVIEEKDVVYKQFPVPLINRLEKHYLDMNTVLQPWQKS
IVQELQQWAHEFADVKADQFIARHKYSPADVFIGYHSDACASVVLQAVERQGCRDLTEEL
YRKVSEEARSILLDCATPDAVVRLSGSSLGSFTAKQLSQEYYYAQQHNSFVDFLQAHLRM
THHECRAVFTEITTFSRLLTGNDCDVLASELRGLASKPVVLSLQQYDTEYSFLKDVRSWL
TNPGKRKVLVIQADFDDGTRSAQLVASAKYTAINEINKTQGTKDFVFVYFVTKLSRMGSG
TSYVGFHGGLWRSVHIDDLRRSTIMASDVTKLQNVTISQLFKPEDKPEQEEMEIETSQSK
ELAEEQMEVEDSEEMKKASDPRSCDCSQFLDTTRLVQSCVQGAVGMLRDQNESCARNMRR
VTILLDLLNEDNTRNASFLRESKMRLHVLLNKQEENQVRSLKEWVTREAANQDALQEAGT
FRHTLWKRVQDVVTPILASMIAHIDRDGNLELLAQPDSPAWVQDLWMFIYSDIKFLNISL
VLNNTRSNSEMSFILVQSHMNLLKDAYNAVPFSWRIRDYLEELWVQAQYITDTEGLSKKF
VEIFQKTPLGVFLAQFPVAQQQKLLQSYLKDFLLLTMKVSSREELMFLQMALWSCLRELQ
EASGTPDETYKFPLSLPWVHLAFQHFRTRLQNFSRILTIHPQVLSSLSQAAEKHSLAGCE
MTLDAFAAMACAEMLKGDLLKPSPKAWLQLVKNLSTPLELVCSEGYLCDSGSMTRSVIQE
VRALWNRIFSIALFVEHVLLGTESHIPELSPLVTTYVSLLDKCLEEDSNLKTCRPFVAVM
TTLCDCKDKASKKFSRFGIQPCFICHGDAQDPVCLPCDHVYCLRCIQTWLIPGQMMCPYC
LTDLPDKFSPTVSQDHRKAIEKHAQFRHMCNSFFVDLVSTMCFKDNTPPEKSVIDTLLSL
LFVQKELLRDASQKHREHTKSLSPFDDVVDQTPVIRSVLLKLLLKYSFHEVKDYIQNYLT
QLEKKAFLTEDKTELYLLFISCLEDSVHQKTSAGCRNLEQVLREEGHFLRTYSPGLQGQE
PVRIASVEYLQEVARVRLCLDLAADFLSELQEGSELAEDKRRFLKHVEEFCTRVNNDWHR
VYLVRKLSSQRGMEFVQSFSKQGHPCQWVFPRKVIAQQKDHVSLMDRYLVHGNEYKAVRD
ATAKAVLECKTLDIGNALMACRSPKPQQTAYLLLALYTEVAALYRSPNGSLHPEAKQLEA
VNKFIKESKILSDPNIRCFARSLVDNTLPLLKIRSANSILKGTVTEMAVHVATILLCGHN
QILKPLRNLAFYPVNMANAFLPTMPEDLLVHARTWRGLENVTWYTCPRGHPCSVGECGRP
MQESTCLDCGLPVGGLNHTPHEGFSAIRNNEDRTQTGHVLGSPQSSGVAEVSDRGQSPVV
FILTRLLTHLAMLVGATHNPQALTVIIKPWVQDPQGFLQQHIQRDLEQLTKMLGRSADET
IHVVHLILSSLLRVQSHGVLNFNAELSTKGCRNNWEKHFETLLLRELKHLDKNLPAINAL
ISQDERISSNPVTKIIYGDPATFLPHLPQKSIIHCSKIWSCRRKITVEYLQHIVEQKNGK
ETVPVLWHFLQKEAELRLVKFLPEILALQRDLVKQFQNVSRVEYSSIRGFIHSHSSDGLR
KLLHDRITIFLSTWNALRRSLETNGEIKLPKDYCCSDLDLDAEFEVILPRRQGLGLCGTA
LVSYLISLHNNMVYTVQKFSNEDNSYSVDISEVADLHVISYEVERDLNPLILSNCQYQVQ
QGGETSQEFDLEKIQRQISSRFLQGKPRLTLKGIPTLVYRRDWNYEHLFMDIKNKMAQSS
LPNLAISTISGQLQSYSDACEALSIIEITLGFLSTAGGDPGMDLNVYIEEVLRMCDQTAQ
VLKAFSRCQLRHIIALWQFLSAHKSEQRLRLNKELFREIDVQYKEELSTQHQRLLGTFLN
EAGLDAFLLELHEMIVLKLKGPRAANSFNPNWSLKDTLVSYMETKDSDILSEVESQFPEE
ILMSSCISVWKIAATRKWDRQSRGGGHHHHHHHHHH
Sequence of entity 2 (B), FASTA
>9I1J_2 Ubiquitin-conjugating enzyme E2 L3 (chains B)
GWSHPQFEKPGSMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDK
GAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSL
IALVNDPQPEHPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P22
ZNZinc ionZn2
MGMagnesium ionMg1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31

Primary citation

ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213. Ahel, J., Balci, A., Faas, V. et al. Nat Commun (2025) 16:4414-4414. DOI 10.1038/s41467-025-59444-4 · PubMed

Other PDB entries of the same protein (UniProt E9Q555), best resolution first:

Browse structure collections

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