7OIM: Mouse RNF213, with mixed nucleotides bound

Mouse RNF213, with mixed nucleotides bound. Determined by electron microscopy at 4.0 Å resolution. Released 1 Jun 2022.

Method
Electron microscopy
Resolution
4.0 Å
Organism
Mus musculus
Chains
1
Atoms
35,597
Mol. weight
554.24 kDa
Ligands
AGS, ADP, ZN, MG
Released
1 Jun 2022

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

Secondary structure: helices and β-sheets

7OIM contains 238 α-helices and 80 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: 238 helices, 80 β-strands

ElementResiduesLengthSheet
α-helix493-51119
α-helix518-53417
α-helix555-56612
α-helix570-5734
α-helix593-60311
α-helix611-6133
α-helix614-6174
α-helix629-6357
α-helix636-6383
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-helix760-77112
α-helix781-80020
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-helix1045-10484
α-helix1054-107118
β-strand107911
α-helix1080-10889
α-helix1090-110112
α-helix1114-114229
β-strand1149-115132
α-helix1155-11584
β-strand116611
α-helix1167-11704
α-helix1191-120212
α-helix1207-121711
β-strand1231-123332
α-helix1234-12374
α-helix1238-12425
α-helix1243-125614
α-helix1263-12697
α-helix1271-12733
α-helix1278-128811
α-helix1299-132830
α-helix1339-13457
α-helix1364-13674
α-helix1368-13703
α-helix1378-13869
α-helix1389-13979
α-helix1401-14033
α-helix1404-141411
α-helix1419-143921
α-helix1448-146316
α-helix1468-14769
α-helix1479-14868
α-helix1498-15069
β-strand1508-151143
β-strand1526-153053
β-strand1541-154333
α-helix1545-155612
α-helix1564-159330
β-strand1602-160653
β-strand1613-161643
β-strand1625-162733
α-helix1631-165727
α-helix1662-16643
α-helix1668-167710
α-helix1685-16906
α-helix1700-17089
α-helix1714-172512
α-helix1730-17323
α-helix1737-174913
α-helix1761-177414
β-strand1793-179644
α-helix1799-18013
α-helix1803-18108
α-helix1816-18183
β-strand1824-182634
α-helix1833-184311
β-strand1853-185754
α-helix1859-18613
α-helix1864-188017
β-strand1887-189264
α-helix1901-19044
α-helix1906-19083
β-strand1909-191024
α-helix1918-192811
α-helix1939-19413
β-strand1948-195365
α-helix1960-197314
β-strand1982-198765
α-helix1994-20018
β-strand2015-202065
α-helix2028-20325
α-helix2033-20375
β-strand2040-204236
β-strand2048-205036
β-strand2056-206275
α-helix2081-20844
β-strand2090-209235
α-helix2117-21204
α-helix2123-213614
α-helix2155-216410
α-helix2173-219220
α-helix2195-22028
α-helix2208-222316
α-helix2251-22544
β-strand2266-226947
β-strand2276-227947
β-strand2282-228548
β-strand2291-229448
α-helix2309-231810
α-helix2331-234212
α-helix2359-237315
β-strand2377-238049
α-helix2388-239912
β-strand2407-241159
α-helix2418-243821
β-strand2444-244859
α-helix2456-24638
β-strand2467-2468210
β-strand2471-2472210
α-helix2473-24742
β-strand2480-248569
α-helix2486-24883
β-strand2490111
α-helix2491-24922
α-helix2493-24997
β-strand2504112
β-strand2516113
β-strand2521113
α-helix2522-25243
β-strand2525111
α-helix2531-25333
α-helix2537-25393
β-strand2541-254229
α-helix2551-256212
α-helix2572-258817
α-helix2606-26149
α-helix2619-262911
α-helix2643-26508
α-helix2651-26555
α-helix2661-26688
α-helix2674-26763
α-helix2679-269517
α-helix2698-26992
α-helix2707-272115
β-strand2726114
β-strand2729115
α-helix2737-274610
α-helix2757-27593
β-strand2763-2767516
α-helix2776-279015
β-strand2799-2803516
α-helix2817-28193
α-helix2821-28244
β-strand2841-2842216
β-strand2843114
β-strand2848112
β-strand2859114
β-strand2862115
α-helix2863-28664
α-helix2868-287710
α-helix2884-28885
α-helix2893-290614
α-helix2914-293118
α-helix2937-294711
α-helix2956-29627
α-helix2975-29839
β-strand3002-3006517
α-helix3011-30144
α-helix3015-30195
α-helix3024-30252
β-strand3026-3028317
α-helix3038-305518
β-strand3059-3061317
α-helix3074-30763
β-strand3086-3091618
β-strand3096-3101618
β-strand3107-3112617
α-helix3113-31186
α-helix3123-31275
β-strand3129-3131317
α-helix3141-315818
β-strand3160119
α-helix3173-31764
β-strand3177120
α-helix3184-319613
α-helix3204-321815
β-strand3221120
α-helix3223-32286
α-helix3229-32313
β-strand3232119
α-helix3237-32448
α-helix3245-32495
α-helix3255-32639
β-strand3272-3279821
α-helix3282-32843
α-helix3288-32947
β-strand3304-3307421
α-helix3314-332512
β-strand3332-3339821
α-helix3349-336416
β-strand3371-3378821
β-strand3398-3400321
α-helix3406-34072
β-strand3410122
α-helix3414-34196
α-helix3422-34265
β-strand3475122
α-helix3477-348913
β-strand3493123
α-helix3502-351110
α-helix3518-353821
α-helix3549-35546
α-helix3557-35637
α-helix3566-358924
α-helix3596-35994
α-helix3605-361410
α-helix36391
β-strand3640123
α-helix36411
α-helix3658-367518
α-helix3681-369010
α-helix3693-36986
α-helix3703-372119
α-helix3728-374518
α-helix3763-378321
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-strand3958-3959224
β-strand3965-3966224
α-helix3968-39747
α-helix3987-39893
β-strand3996124
α-helix4001-402525
α-helix4036-40449
β-strand4047125
β-strand4064125
β-strand4080126
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-helix4297-43048
α-helix4310-433021
α-helix4343-435210
α-helix4359-436911
α-helix4385-440218
α-helix4406-44083
α-helix4409-44168
α-helix4418-44203
α-helix4523-454119
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-strand4751127
α-helix4752-47565
α-helix4762-478221
α-helix4786-47894
β-strand4808127
α-helix4821-484424
α-helix4860-48623
α-helix4868-48725
α-helix4873-48775
β-strand4880-4883428
β-strand4884126
β-strand4891-4894428
α-helix4896-49049
α-helix4931-494010
α-helix4948-49569
α-helix4961-497919
α-helix4990-49934
α-helix5004-50107
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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase RNF213Aprotein4836Mus musculusE9Q555
Sequence of entity 1 (A), FASTA
>7OIM_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

Ligands and cofactors

IDNameFormulaCopies
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S1
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21
ZNZinc ionZn2
MGMagnesium ionMg1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31

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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