9I1I: Mouse RNF213

Cryo-EM structure of mouse RNF213 (WB3/WB4 + ATP). Determined by electron microscopy at 4.5 Å resolution. Released 10 Dec 2025.

Method
Electron microscopy
Resolution
4.5 Å
Organism
Mus musculus
Chains
1
Atoms
36,852
Mol. weight
587.71 kDa
Ligands
ZN, MG, ATP
Released
10 Dec 2025

Explore 9I1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I1I contains 246 α-helices and 92 β-strands across 1 chain. 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: 246 helices, 92 β-strands

ElementResiduesLengthSheet
β-strand347-357111
α-helix358-3603
β-strand369-37352
α-helix375-3773
β-strand383-38862
β-strand389-39351
β-strand398-408111
α-helix409-4113
β-strand416-42272
β-strand433-43422
β-strand449-45242
β-strand463-47191
α-helix488-51225
α-helix518-53619
β-strand539-54132
β-strand545-54732
α-helix549-5513
α-helix555-57420
α-helix579-5813
α-helix591-60515
α-helix611-6133
α-helix614-6207
α-helix629-6357
α-helix636-6394
α-helix644-65512
α-helix663-6664
α-helix667-6726
α-helix681-6822
α-helix689-6924
α-helix701-7044
α-helix712-7198
α-helix722-7254
α-helix729-7357
α-helix740-7423
α-helix743-7497
α-helix751-7566
α-helix760-77415
α-helix776-7783
α-helix782-79918
α-helix804-8063
α-helix811-82616
α-helix836-84914
α-helix864-88825
α-helix909-9168
α-helix930-93910
α-helix943-9508
α-helix963-98119
α-helix995-100814
α-helix1022-10309
α-helix1034-104310
α-helix1053-107018
β-strand107913
α-helix1080-10889
α-helix1090-110112
α-helix1114-114330
β-strand1148-115144
α-helix1155-11584
β-strand116613
α-helix1167-11704
β-strand117215
β-strand118215
α-helix1191-120212
α-helix1207-121711
α-helix1218-12203
β-strand1230-123344
α-helix1234-12374
α-helix1238-12425
α-helix1243-125816
α-helix1263-12697
α-helix1278-128710
α-helix1299-132931
α-helix1339-13457
α-helix1364-13685
α-helix1378-13869
α-helix1388-139710
α-helix1404-141411
α-helix1419-143921
α-helix1448-146215
α-helix1468-14769
α-helix1479-14868
α-helix1496-150611
β-strand1508-151146
α-helix1522-15243
β-strand1526-153056
β-strand1541-154336
α-helix1545-155612
α-helix1564-159330
β-strand1602-160656
β-strand1613-161646
β-strand1625-162626
α-helix1631-165727
α-helix1662-16643
α-helix1668-167710
α-helix1685-16917
α-helix1700-17089
α-helix1713-173220
α-helix1736-174914
α-helix1761-177414
α-helix1782-17843
β-strand1793-179647
α-helix1802-18098
α-helix1810-18123
α-helix1817-18193
β-strand1824-182637
α-helix1833-184311
β-strand1853-185757
α-helix1859-18613
α-helix1864-188017
β-strand1887-189267
α-helix1900-19045
β-strand190917
α-helix1918-192811
α-helix1930-19323
α-helix1938-19403
β-strand1948-195368
α-helix1960-197314
β-strand1984-198748
α-helix1994-20018
α-helix2002-20043
β-strand2017-202048
α-helix2028-20325
α-helix2033-20375
β-strand2040-204129
β-strand2049-205029
β-strand2057-206268
α-helix2082-20854
β-strand2090-209238
α-helix2096-20983
α-helix2117-21204
α-helix2123-213614
α-helix2155-216612
α-helix2173-219220
α-helix2195-22028
α-helix2208-222316
α-helix2251-22544
β-strand2266-2269410
β-strand2276-2279410
β-strand2282-2285411
β-strand2291-2294411
α-helix2309-231810
α-helix2326-23283
α-helix2331-234111
α-helix2358-237316
β-strand2377-2380412
α-helix2388-239912
β-strand2407-2411512
α-helix2418-243922
β-strand2444-2448512
α-helix2456-24638
β-strand2467-2468213
β-strand2471-2472213
α-helix2473-24742
β-strand2480-2485612
β-strand2490114
α-helix2491-24922
α-helix2493-25008
α-helix2510-25123
β-strand2516115
β-strand2521115
α-helix2522-25243
β-strand2525114
α-helix2530-25334
β-strand2542112
α-helix2551-256111
α-helix2572-258817
α-helix2602-261413
α-helix2616-263015
α-helix2633-26353
α-helix2643-265311
α-helix2661-26688
α-helix2674-26763
α-helix2679-269618
α-helix2698-26992
α-helix2707-272216
β-strand2726116
β-strand2729117
α-helix2736-274611
α-helix2755-27595
β-strand2762-2763218
β-strand2766-2767216
α-helix2776-278914
β-strand2798-2799218
β-strand2801-2803316
α-helix2807-28126
α-helix2817-28193
α-helix2821-28277
β-strand2841-2843316
α-helix2854-28574
β-strand2859116
β-strand2862117
α-helix2868-287811
α-helix2879-28813
α-helix2883-28897
α-helix2893-290614
α-helix2914-293118
α-helix2937-294711
α-helix2956-29638
α-helix2975-29839
α-helix2999-30002
β-strand3001-3006619
α-helix3011-30144
α-helix3015-30195
α-helix3024-30252
β-strand3026-3027219
α-helix3038-305518
β-strand3059-3061319
β-strand3082120
β-strand3085120
β-strand3086-3091621
β-strand3096-3101621
β-strand3107-3112619
α-helix3113-31197
α-helix3122-31276
β-strand3128-3132519
α-helix3141-315515
β-strand3160122
α-helix3170-31723
α-helix3173-31764
β-strand3177123
α-helix3184-319613
α-helix3204-321815
β-strand3221123
α-helix3223-32286
α-helix3229-32313
β-strand3232122
α-helix3238-32447
α-helix3245-32495
α-helix3255-326410
β-strand3272-3279824
α-helix3282-32843
α-helix3287-32948
β-strand3304-3307424
α-helix3314-332613
β-strand3332-3339824
α-helix3349-336416
β-strand3371-3378824
β-strand3397-3401524
β-strand3410125
α-helix3414-34196
α-helix3423-34264
β-strand3475125
α-helix3477-349014
β-strand3493126
α-helix3502-351211
α-helix3518-353922
α-helix3549-35557
α-helix3557-35626
α-helix3566-358924
α-helix3596-35994
α-helix3605-361511
β-strand3640126
α-helix3659-367517
α-helix3681-369111
α-helix3693-36997
α-helix3703-372119
α-helix3728-374417
α-helix3762-378423
α-helix3788-379912
α-helix3808-382215
α-helix3829-383810
α-helix3840-38467
α-helix3857-388933
α-helix3895-390713
α-helix3918-393922
α-helix3944-39474
α-helix3953-39542
β-strand3958-3959227
β-strand3965-3966227
α-helix3968-39747
β-strand3981128
β-strand3988128
β-strand3996127
α-helix4001-402525
α-helix4026-40283
α-helix4036-40449
α-helix4083-40897
α-helix4093-40953
α-helix4097-411014
α-helix4117-413822
α-helix4144-415512
α-helix4172-419726
α-helix4205-421814
α-helix4222-423514
α-helix4238-42447
α-helix4252-42543
α-helix4258-42614
α-helix4269-42713
α-helix4280-429213
α-helix4297-43048
α-helix4310-433021
α-helix4343-435210
α-helix4359-436911
α-helix4386-440217
α-helix4408-44169
α-helix4523-454119
α-helix4545-45517
α-helix4559-457517
α-helix4582-459514
α-helix4596-45983
α-helix4614-463219
α-helix4639-46479
α-helix4666-46683
α-helix4673-46753
α-helix4692-470110
α-helix4709-47168
α-helix4718-47214
α-helix4724-47263
α-helix4727-474014
β-strand4751129
α-helix4752-47576
α-helix4762-478221
β-strand4808129
α-helix4810-48123
α-helix4821-484121
α-helix4842-48465
β-strand4852-4853230
α-helix4868-48725
α-helix4873-48775
β-strand4881-4883331
β-strand4891-4893331
α-helix4896-49049
β-strand4913-4914230
α-helix4931-494010
α-helix4945-49473
α-helix4948-495710
α-helix4962-497918
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-helix5100-51078
α-helix5117-51204
α-helix5132-514817

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase RNF213Aprotein5161Mus musculusE9Q555
Sequence of entity 1 (A), FASTA
>9I1I_1 E3 ubiquitin-protein ligase RNF213 (chains A)
MECPQCGHVSSEKAPKFCSECGQKLPSAATVQGDLKNDNTLVVSSTPEGKTEQGAVLREE
EVLLSSTDPGKELEKPEESDSNASWTTQMSKKEKRRRKRQGTISSSEAPSSGLWSLDMPP
SPGSHNSALPQNQAQQGGAASQPGHPLDTENMPMEDGFVHTEGSGSPLQGQAAERTDAQS
NLAPSDLAEVKDLNTSKPSVDKGLPLDGGPALSAFKGHPKMTDASQKAPLPESKGETSGQ
EKKVPPIDAAASPVKTAGKETGEDVRKPKPSPVSPVASKHGDQEAELKGKLATPVRKSNE
GGNTQPEDQRKPGEGRNFAAAVKTQQAAAPQQAAAPEPTSAFNPRDTVTVYFHAIVSRHF
GFNPEEHKVYVRGGEGLGQKGWTDACEMYCTQDLHDLGSLVEGKMDIPRQSLDKPIPYKY
VIHRGGSSKDTVEYEFIYEQAQKKGEHVNRCLRVVSTSLGNGDWHQYDDIICMRSTGFFQ
QAKNRILDSTRKELLKGKKQAAVVMLDRIFSVLQPWSDINLQSFMTQFLQFYSVVREPMI
HDGRARKWTSLQYEEKEVWTNLWEHVKKQMAPFLEGKSGESLPADCPVRSKLTLGLSILF
MVEAAEFTVPKKDLDSLCYLLIPSAGSPEALHSDLSPVLRIRQRWRIYLTNLCLRCIDER
CDRWLGILPLLHTCMQKSPPKKNSKSQPEDTWAGLEGISFSEFRDKAPTRSQPLQFMQSK
MALLRVDEYLFRSWLSVVPLESLSSYLENSIDYLSDVPVRVLDCLQGISYRLPGLRKISN
QNMKKDVENVFKMLMHLVDIYQHRIFGENLLQIYLTECLTLHETVCNITANHQFFEIPAL
SAELICKLLELSPPGHTDEGLPEKSYEDLVTSTLQEALATTRNWLRSLFKSRMLSISSAY
VRLTYSEEMAVWRRLVEIGFPEKHGWKGSLLGDMEGRLKQEPPRLQISFFCSSQCRDGGL
HDSVSRSFEKCVIEAVSSACQSQTSVLEGLSCQDLQKFGTLLSAVITKSWPVHNGEPVFD
VDEIFKYLLKWPDVRQLFELCGTNEKIIDNITEEGRQLMATAESVFQKVAGELENGTIVV
GQLELILEHQSQFLDIWNLNRRRLPSQEKACDVRSLLKRRRDDLLFLKQEKRYVESLLRQ
LGRVKHLVQVDFGNIEIIHSQDLSNKKLNEAVIKLPNSSSYKRETHYCLSPDIREMASKL
DSLKDSHIFQDFWQETAESLNTLDKDPRELKVSLPEVLEYLYNPCYDNFYTLYENLKSGK
ITFAEVDAIFKDFVDKYDELKNDLKFMCTMNPQDQKGWISERVGQIKEYHTLHQAVSSAK
VILQVRRALGVTGDFSVLNPLLNFADSFEDFGNEKLDQISPQFIKAKQLLQDISEPRQRC
LEELARQTELVAWLHKALEDINELKVFVDLASISAGENDIDVDRVACFHDAVQGYASLLY
KMDERTNFSDFMNHLQELWRALDNDQHLPDKLKDSARNLEWLKTVKESHGSVELSSLSLA
TAINSRGVYVIEAPKDGQKISPDTVLRLLLPDGHGYPEALRTYSTEELKELLNKLMLMSG
KKDHNSNTEVEKFSEVFSNMQRLVHVFIKLHCAGNMLFRTWTAKVYCCPDGGIFMNFGLE
LLSQLTEKGDVIQLLGALCRQMEDFLDNWKTVVAQKRAEHFYLNFYTAEQLVYLSSELRK
PRPSEAALMMLSFIKGKCTVQDLVQATSACESKADRYCLREVMKKLPQQLLSEPSLMGKL
QVIMMQSLVYMSAFLPHCLDLDALGRCLAHLATMGGTPVERPLPKGLQAGQPNLILCGHS
EVLPAALAIYMQAPRQPLPTFDEVLLCTPATTIEEVELLLRRCLTSGSQGHKVYSLLFAD
QLSYEVGCQAEEFFQSLCTRAHREDYQLVILCDAAREHCYIPSTFSQYKVPLVPQAPLPN
IQAYLQSHYQVPKRLLSAATVFRDGLCVGIVTSERAGVGKSLYVNTLHTKLKAKLRDETV
PLKIIRLTEPHLDENQVLSALLPFLKEKYQKMPVIFHIDISTSVQTGIPIFLFKLLILQY
LMDINGKIWRRSPGHLYLVEIPQGLSVQPKRSSKLNARAPLFKFLDLFPKVTCRPPKEVI
DMELTPERSHTDPAMDPVEFCSEAFQRPYQYLKRFHQQQNLDTFQYEKGSVEGSPEECLQ
HFLIYCGLINPSWSELRNFAWFLNCQLKDCEASIFCKSAFTGDTLRGFKNFVVTFMILMA
RDFATPTLHTSDQSPGRQSVTIGEVVEEDLAPFSLRKRWESEPHPYVFFNGDHMTMTFIG
FHLETNNNGYVDAINPSNGKVIKKDVMTKELFDGLRLQRVPFNIDFDNLPRYEKLERLCL
ALGIEWPIDPDETYELTTDNMLKILAIEMRFRCGIPVIIMGETGCGKTRLIKFLSDLKRG
SVEAETMKLVKVHGGTTPSMIYSKVKEAERTAFSNKAQHKLDTILFFDQANTTEAVSCIK
EILCDRTVDGEHLHEDSGLHIIAACNPYRKHSQEMILRLESAGLGYRVSAEETADRLGSI
PLRQLVYRVHALPPSLIPLVWDFGQLNDSAEKLYIQQIVQRLVDSVSVNPSETCVIADVL
SASQMFMRKRENECGFVSLRDVERCVKVFRWFHDHSDMLLKELDKFLHESSDSTHTFERD
PVLWSLVMAIGVCYHASLEEKASYRTAIARCFPKPYNSSRAILDEVTHVQDLFLRGAPIR
TNIARNLALKENVFMMVICIELKIPLFLVGKPGSSKSLAKIIVADAMQGQAAFSELFRCL
KQVHLVSFQCSPHSTPQGIISTFKQCARFQQGKDLGQYVSVVVLDQVGLAEDSPKMPLKT
LHPLLEDGCIEDDPAPYKKVGFVGISNWALDPAKMNRGIFVSRGSPNEKELIESAEGICS
SDRLVQDKIRGYFAPFAKAYETVCQKQDKEFFGLRDYYSLIKMVFAKAKASKRGLSPQDI
THAVLRNFSGKDNIQALSIFTASLPEARYKEEVSTVELIKQNIYPGPQASSRGLDGAESR
YLLVLTRNYVALQILQQTFFEGQQPEIIFGSSFPQDQEYTQICRNINRVKICMETGKMVV
LLNLQNLYESLYDALNQYYVYLGGQKYVDLGLGTHRVKCRVHTAFRLIVIEEKDVVYKQF
PVPLINRLEKHYLDMNTVLQPWQKSIVQELQQWAHEFADVKADQFIARHKYSPADVFIGY
HSDACASVVLQAVERQGCRDLTEELYRKVSEEARSILLDCATPDAVVRLSGSSLGSFTAK
QLSQEYYYAQQHNSFVDFLQAHLRMTHHECRAVFTEITTFSRLLTGNDCDVLASELRGLA
SKPVVLSLQQYDTEYSFLKDVRSWLTNPGKRKVLVIQADFDDGTRSAQLVASAKYTAINE
INKTQGTKDFVFVYFVTKLSRMGSGTSYVGFHGGLWRSVHIDDLRRSTIMASDVTKLQNV
TISQLFKPEDKPEQEEMEIETSQSKELAEEQMEVEDSEEMKKASDPRSCDCSQFLDTTRL
VQSCVQGAVGMLRDQNESCARNMRRVTILLDLLNEDNTRNASFLRESKMRLHVLLNKQEE
NQVRSLKEWVTREAANQDALQEAGTFRHTLWKRVQDVVTPILASMIAHIDRDGNLELLAQ
PDSPAWVQDLWMFIYSDIKFLNISLVLNNTRSNSEMSFILVQSHMNLLKDAYNAVPFSWR
IRDYLEELWVQAQYITDTEGLSKKFVEIFQKTPLGVFLAQFPVAQQQKLLQSYLKDFLLL
TMKVSSREELMFLQMALWSCLRELQEASGTPDETYKFPLSLPWVHLAFQHFRTRLQNFSR
ILTIHPQVLSSLSQAAEKHSLAGCEMTLDAFAAMACAEMLKGDLLKPSPKAWLQLVKNLS
TPLELVCSEGYLCDSGSMTRSVIQEVRALWNRIFSIALFVEHVLLGTESHIPELSPLVTT
YVSLLDKCLEEDSNLKTCRPFVAVMTTLCDCKDKASKKFSRFGIQPCFICHGDAQDPVCL
PCDHVYCLRCIQTWLIPGQMMCPYCLTDLPDKFSPTVSQDHRKAIEKHAQFRHMCNSFFV
DLVSTMCFKDNTPPEKSVIDTLLSLLFVQKELLRDASQKHREHTKSLSPFDDVVDQTPVI
RSVLLKLLLKYSFHEVKDYIQNYLTQLEKKAFLTEDKTELYLLFISCLEDSVHQKTSAGC
RNLEQVLREEGHFLRTYSPGLQGQEPVRIASVEYLQEVARVRLCLDLAADFLSELQEGSE
LAEDKRRFLKHVEEFCTRVNNDWHRVYLVRKLSSQRGMEFVQSFSKQGHPCQWVFPRKVI
AQQKDHVSLMDRYLVHGNEYKAVRDATAKAVLECKTLDIGNALMACRSPKPQQTAYLLLA
LYTEVAALYRSPNGSLHPEAKQLEAVNKFIKESKILSDPNIRCFARSLVDNTLPLLKIRS
ANSILKGTVTEMAVHVATILLCGHNQILKPLRNLAFYPVNMANAFLPTMPEDLLVHARTW
RGLENVTWYTCPRGHPCSVGECGRPMQESTCLDCGLPVGGLNHTPHEGFSAIRNNEDRTQ
TGHVLGSPQSSGVAEVSDRGQSPVVFILTRLLTHLAMLVGATHNPQALTVIIKPWVQDPQ
GFLQQHIQRDLEQLTKMLGRSADETIHVVHLILSSLLRVQSHGVLNFNAELSTKGCRNNW
EKHFETLLLRELKHLDKNLPAINALISQDERISSNPVTKIIYGDPATFLPHLPQKSIIHC
SKIWSCRRKITVEYLQHIVEQKNGKETVPVLWHFLQKEAELRLVKFLPEILALQRDLVKQ
FQNVSRVEYSSIRGFIHSHSSDGLRKLLHDRITIFLSTWNALRRSLETNGEIKLPKDYCC
SDLDLDAEFEVILPRRQGLGLCGTALVSYLISLHNNMVYTVQKFSNEDNSYSVDISEVAD
LHVISYEVERDLNPLILSNCQYQVQQGGETSQEFDLEKIQRQISSRFLQGKPRLTLKGIP
TLVYRRDWNYEHLFMDIKNKMAQSSLPNLAISTISGQLQSYSDACEALSIIEITLGFLST
AGGDPGMDLNVYIEEVLRMC

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2
MGMagnesium ionMg1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P32

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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