7OIK: E3 ubiquitin-protein ligase RNF213

Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized. Determined by electron microscopy at 3.5 Å resolution. Released 1 Jun 2022.

Method
Electron microscopy
Resolution
3.5 Å
Organisms
Mus musculus, Homo sapiens
Chains
2
Atoms
36,779
Mol. weight
606.41 kDa
Ligands
ATP, MG, ZN
Released
1 Jun 2022

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

Secondary structure: helices and β-sheets

7OIK contains 244 α-helices and 92 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: 237 helices, 83 β-strands

ElementResiduesLengthSheet
α-helix493-51220
α-helix518-53417
α-helix556-57520
α-helix592-60312
α-helix611-62111
α-helix629-6357
α-helix644-65512
α-helix663-6664
α-helix668-6714
α-helix681-6822
α-helix689-6935
α-helix700-7023
α-helix712-7198
α-helix721-7255
α-helix729-7357
α-helix743-7486
α-helix751-7566
α-helix760-77415
α-helix781-79919
α-helix811-82616
α-helix836-84914
α-helix852-8543
α-helix865-88824
α-helix909-9168
α-helix930-9389
α-helix943-9508
α-helix963-98119
α-helix995-100915
α-helix1022-10309
α-helix1033-104311
α-helix1054-107118
β-strand107911
α-helix1080-10889
α-helix1090-110011
α-helix1114-114229
β-strand1149-115022
α-helix1155-11584
β-strand116611
α-helix1167-11704
α-helix1192-120211
α-helix1207-121711
β-strand1231-123222
α-helix1234-12374
α-helix1238-12425
α-helix1243-125816
α-helix1263-12697
α-helix1271-12733
α-helix1278-128811
α-helix1299-132830
α-helix1339-13457
α-helix1364-13674
α-helix1378-13869
α-helix1389-13979
α-helix1404-141411
α-helix1419-143921
α-helix1448-146316
α-helix1468-14769
α-helix1479-14868
α-helix1497-150610
β-strand1508-151143
β-strand1526-153053
β-strand1541-154443
α-helix1545-155612
α-helix1564-159330
β-strand1602-160653
β-strand1612-161653
β-strand1625-162733
α-helix1631-165929
α-helix1662-16654
α-helix1668-167811
α-helix1685-16906
α-helix1691-16933
α-helix1700-17089
α-helix1714-172512
α-helix1727-17304
α-helix1736-174914
α-helix1751-17533
α-helix1761-177414
β-strand178014
α-helix1782-17843
β-strand1792-179655
α-helix1799-18013
α-helix1803-18097
α-helix1817-18193
β-strand1824-182635
α-helix1833-184311
β-strand185114
β-strand1853-185755
α-helix1859-18613
α-helix1864-188017
β-strand1887-189265
α-helix1901-19044
α-helix1906-19083
β-strand190915
α-helix1918-192912
α-helix1938-19414
β-strand1948-195366
α-helix1960-197314
β-strand1982-198766
α-helix1994-20018
β-strand2015-202066
α-helix2028-20325
α-helix2033-20375
β-strand2040-204237
β-strand2048-205037
β-strand205318
β-strand205518
β-strand2056-206276
α-helix2081-20844
α-helix2085-20873
β-strand2090-209346
α-helix2117-21204
α-helix2123-213614
α-helix2155-216511
α-helix2173-219220
α-helix2195-22028
α-helix2208-222316
α-helix2251-22544
β-strand2266-226949
β-strand2276-227949
β-strand2282-2285410
β-strand2290-2294510
β-strand2307-2308210
α-helix2309-23179
α-helix2331-234111
α-helix2358-237316
β-strand2377-2380411
α-helix2388-239912
β-strand2407-2411511
α-helix2418-243922
β-strand2443-2448611
α-helix2456-24638
β-strand2467-2468212
β-strand2471-2472212
α-helix2473-24742
β-strand2479-2485711
β-strand2490113
α-helix2491-24922
α-helix2493-25008
β-strand2516114
β-strand2521114
α-helix2522-25243
β-strand2525113
α-helix2530-25334
β-strand2540-2541211
α-helix2551-256313
α-helix2565-25673
α-helix2572-258817
α-helix2601-261414
α-helix2618-263013
α-helix2643-26508
α-helix2651-26555
α-helix2661-26688
α-helix2674-26763
α-helix2679-269618
α-helix2698-26992
α-helix2707-272115
β-strand2726-2729415
α-helix2738-27469
β-strand2762-2768715
α-helix2776-279015
β-strand2798-2804715
α-helix2818-28203
α-helix2821-28244
β-strand2841-2846615
β-strand2859-2862415
α-helix2868-287912
α-helix2884-28885
α-helix2889-28924
α-helix2893-290614
α-helix2914-293118
α-helix2937-294711
α-helix2956-29605
α-helix2975-29839
β-strand3002-3006516
α-helix3011-30144
α-helix3015-30195
β-strand3026-3028316
α-helix3038-305518
β-strand3059-3061316
α-helix3072-30765
β-strand3080-3082317
β-strand3085-3092817
β-strand3095-3101717
β-strand3107-3112616
α-helix3113-31197
α-helix3125-31273
β-strand3130-3132316
α-helix3141-315818
β-strand3160118
α-helix3170-31723
α-helix3173-31764
β-strand3177119
α-helix3184-319613
α-helix3205-321814
β-strand3221119
α-helix3223-32286
α-helix3229-32313
β-strand3232118
α-helix3237-32448
α-helix3245-32495
α-helix3255-32628
β-strand3272-3279820
α-helix3282-32843
α-helix3288-32947
β-strand3304-3307420
α-helix3308-33103
α-helix3314-332512
β-strand3332-3339820
α-helix3349-336416
β-strand3371-3378820
β-strand3397-3400420
α-helix3406-34072
β-strand3410121
α-helix3414-34196
α-helix3422-34254
β-strand3475121
α-helix3477-348913
β-strand3493122
α-helix3502-351110
α-helix3518-353821
α-helix3549-35546
α-helix3557-35637
α-helix3566-358924
α-helix3596-35994
α-helix3605-361410
α-helix36391
β-strand3640122
α-helix36411
α-helix3658-367518
α-helix3681-369010
α-helix3693-36986
α-helix3703-372119
α-helix3728-374518
α-helix3762-378322
α-helix3788-379912
α-helix3808-382316
α-helix3829-383810
α-helix3840-38467
α-helix3857-387923
α-helix3880-38845
α-helix3885-38895
α-helix3895-390915
α-helix3918-394023
β-strand3958-3959223
β-strand3965-3966223
α-helix3968-39747
α-helix3987-39893
β-strand3996123
α-helix4000-402526
α-helix4036-40449
β-strand4047124
β-strand4064124
β-strand4080125
α-helix4083-40886
α-helix4093-40953
α-helix4097-411014
α-helix4117-413721
α-helix4143-415513
α-helix4172-419726
α-helix4205-421814
α-helix4223-423513
α-helix4238-42447
α-helix4252-42543
α-helix4257-42615
α-helix4272-42754
α-helix4280-429213
α-helix4297-43037
α-helix4310-433021
α-helix4343-435210
α-helix4359-436911
α-helix4385-440218
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-helix4666-46683
α-helix4692-470110
α-helix4709-47168
α-helix4718-47214
α-helix4724-47263
α-helix4727-474014
β-strand4751126
α-helix4752-47565
α-helix4762-478221
α-helix4786-47894
β-strand4808126
α-helix4821-484424
α-helix4860-48623
α-helix4868-48725
α-helix4873-48775
β-strand4880-4883427
β-strand4884125
β-strand4891-4894427
α-helix4896-49049
α-helix4931-494010
α-helix4948-49569
α-helix4961-497919
β-strand4988128
α-helix4989-49902
α-helix4991-49966
α-helix5004-50107
β-strand5014128
α-helix5015-50173
α-helix5018-503518
α-helix5046-50483
β-strand5049129
α-helix5054-506512
α-helix5069-508315
α-helix5099-51068
α-helix5116-51205
β-strand5130129
α-helix5132-514312
α-helix5144-51485
Chain B: 7 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix1-1717
β-strand22-26530
β-strand34-39630
β-strand50131
β-strand51-56630
β-strand67-70430
β-strand79132
β-strand84130
β-strand85132
α-helix88-903
α-helix101-11313
α-helix123-1319
α-helix133-14715
α-helix1481
β-strand149131
α-helix150-1512

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase RNF213Aprotein5161Mus musculusE9Q555
Ubiquitin-conjugating enzyme E2 L3Bprotein166Homo sapiensP68036 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7OIK_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
SVEAETMKLVKVHGGTTPSMIYSKVKEAERTAFSNKAQHKLDTILFFDEANTTEAVSCIK
EILCDRTVDGEHLHEDSGLHIIAACNPYRKHSQEMILRLESAGLGYRVSAEETADRLGSI
PLRQLVYRVHALPPSLIPLVWDFGQLNDSAEKLYIQQIVQRLVDSVSVNPSETCVIADVL
SASQMFMRKRENECGFVSLRDVERCVKVFRWFHDHSDMLLKELDKFLHESSDSTHTFERD
PVLWSLVMAIGVCYHASLEEKASYRTAIARCFPKPYNSSRAILDEVTHVQDLFLRGAPIR
TNIARNLALKENVFMMVICIELKIPLFLVGKPGSSKSLAKIIVADAMQGQAAFSELFRCL
KQVHLVSFQCSPHSTPQGIISTFKQCARFQQGKDLGQYVSVVVLDEVGLAEDSPKMPLKT
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
Sequence of entity 2 (B), FASTA
>7OIK_2 Ubiquitin-conjugating enzyme E2 L3 (chains B)
GWSHPQFEKPGSMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDK
GAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSL
IALVNDPQPEHPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
MGMagnesium ionMg1
ZNZinc ionZn2

Primary citation

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP. Ahel, J., Fletcher, A.J., Grabarczyk, D. et al. To be published.

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

Browse structure collections

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