8S24: E3 ubiquitin ligase RNF213, determined by cryoEM

Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM. Determined by electron microscopy at 3.0 Å resolution. Released 9 Oct 2024.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Homo sapiens
Chains
1
Atoms
35,357
Mol. weight
597.05 kDa
Ligands
ZN, MG, ATP
Released
9 Oct 2024

Explore 8S24 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S24 contains 257 α-helices and 93 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: 257 helices, 93 β-strands

ElementResiduesLengthSheet
β-strand379-38681
β-strand402-40432
β-strand421-42771
β-strand430-439101
β-strand44713
β-strand450-45232
β-strand48113
β-strand491-49441
β-strand49811
α-helix523-53816
α-helix546-56419
α-helix584-59815
α-helix619-63214
α-helix641-6477
α-helix655-66612
α-helix672-68110
α-helix690-6945
α-helix695-7028
α-helix704-7074
α-helix711-7133
α-helix716-7194
α-helix728-7336
α-helix738-7469
α-helix750-7534
α-helix756-7649
α-helix767-7693
α-helix771-7766
α-helix778-7836
α-helix786-79611
α-helix799-8068
α-helix811-83020
α-helix843-85816
α-helix866-88015
α-helix899-91719
β-strand92314
β-strand93014
α-helix935-9439
α-helix953-96614
α-helix970-97910
α-helix990-100819
α-helix1022-103615
α-helix1044-105310
α-helix1056-106611
α-helix1069-10724
α-helix1076-109823
β-strand110215
α-helix1103-11119
α-helix1113-112412
α-helix1136-116429
α-helix1178-11836
α-helix1186-11883
β-strand119015
α-helix1191-11944
α-helix1215-122612
α-helix1231-12366
α-helix12741
α-helix1275-12795
α-helix1280-129516
α-helix1300-13078
α-helix1308-13103
α-helix1314-13229
α-helix1323-13264
α-helix1341-136525
α-helix1373-13753
α-helix1376-13794
α-helix1385-13895
α-helix1399-14068
α-helix1412-142312
α-helix1426-14349
α-helix1439-145012
α-helix1456-147116
α-helix1473-14764
α-helix1485-150117
α-helix1505-151410
α-helix1516-15249
α-helix1533-154311
β-strand1545-154846
α-helix1550-15512
α-helix1559-15624
β-strand1563-156756
α-helix1568-15703
β-strand1578-158036
α-helix1582-159413
α-helix1604-162825
α-helix1633-16364
β-strand1638-164696
β-strand1649-165466
α-helix1661-16622
β-strand1663-166536
α-helix1669-169729
α-helix1700-17034
α-helix1706-171611
α-helix1721-17222
α-helix1723-17308
α-helix1738-17458
α-helix1751-176919
α-helix1774-178714
α-helix1789-17924
α-helix1799-181214
β-strand1830-183567
α-helix1837-184913
α-helix1855-18562
β-strand1862-186437
α-helix1871-188212
β-strand1891-189557
α-helix1897-18993
α-helix1902-191716
β-strand1925-193177
α-helix1932-19343
α-helix1938-19425
α-helix1944-19463
β-strand1947-194827
α-helix1956-196712
β-strand196818
α-helix1969-19702
α-helix1976-19794
β-strand198418
β-strand1986-199169
α-helix1998-201215
β-strand2020-202569
β-strand2029110
α-helix2032-20398
α-helix2040-20434
β-strand2052-205879
β-strand2064110
α-helix2066-20705
α-helix2071-20755
β-strand2078-2080311
β-strand2086-2088311
β-strand2093-210089
α-helix2123-21264
β-strand2129-213139
α-helix2135-21417
α-helix2156-21594
α-helix2162-217514
α-helix2185-21862
α-helix2194-220411
α-helix2212-223019
α-helix2247-226317
β-strand2305-2308412
β-strand2315-2318412
β-strand2321-2324413
β-strand2329-2333513
β-strand2340-2347813
α-helix2348-23569
α-helix2365-23673
α-helix2370-238011
α-helix2397-241216
β-strand2416-2419414
α-helix2426-243813
β-strand2446-2450514
α-helix2457-247721
β-strand2482-2487614
α-helix2489-24913
α-helix2495-24995
α-helix2500-25045
β-strand2506-2507215
β-strand2510-2511215
α-helix25121
β-strand2518-2524714
β-strand2529116
α-helix2532-25398
β-strand2555-2556217
β-strand2559-2560217
α-helix2561-25633
β-strand2564116
α-helix2570-25723
β-strand2580-2581214
α-helix2584-25863
α-helix2587-260519
α-helix2609-262820
α-helix2638-265316
α-helix2655-266814
α-helix2680-268910
α-helix2690-26945
α-helix2700-27089
α-helix2718-273316
α-helix2746-276015
β-strand2765-2768418
α-helix2776-278510
α-helix2788-27903
α-helix2796-27983
β-strand2801-2808818
α-helix2815-282915
β-strand2837-2844818
α-helix2846-28494
α-helix2857-28593
α-helix2860-28667
α-helix2875-28773
β-strand2880-2885618
α-helix2891-28933
β-strand2898-2901418
α-helix2902-29054
α-helix2907-291711
α-helix2918-29203
α-helix2922-29287
α-helix2929-29313
α-helix2932-294514
α-helix2953-297018
α-helix2973-29753
α-helix2976-298611
α-helix2997-30004
α-helix3014-30229
β-strand3041-3046619
α-helix3050-30589
β-strand3067-3069319
α-helix3080-309617
β-strand3100-3102319
α-helix3113-31164
β-strand3121-3123320
β-strand3126-3133820
β-strand3136-3142720
β-strand3148-3153619
α-helix3154-31607
α-helix3163-31675
β-strand3169-3173519
α-helix3176-31783
α-helix3182-319918
α-helix3214-32174
α-helix3225-323713
α-helix3244-325916
α-helix3264-327310
α-helix3278-32858
α-helix3286-32905
α-helix3296-330510
β-strand3313-3320821
α-helix3323-33253
α-helix3327-333610
α-helix3343-33442
β-strand3345-3348421
α-helix3349-33513
α-helix3355-336612
β-strand3372-3380921
α-helix3387-340418
β-strand3411-3419921
α-helix3428-34292
β-strand3438-3441421
α-helix34541
α-helix3458-34603
α-helix3532-354413
β-strand3547-3549322
α-helix3556-356712
α-helix3573-359523
α-helix3600-36023
α-helix3603-36086
α-helix3611-36177
α-helix3620-364324
α-helix3645-36473
α-helix3648-36536
α-helix3659-367012
α-helix3678-36803
β-strand3693-3695322
α-helix3712-372918
α-helix3735-374511
α-helix3747-37526
α-helix3758-377518
α-helix3781-380020
α-helix3811-382010
α-helix3822-383413
α-helix3836-38416
α-helix3858-387215
α-helix3879-388810
α-helix3890-38967
α-helix3907-392923
α-helix3930-39345
α-helix3937-39404
α-helix3942-39443
α-helix3945-395814
α-helix3968-398922
β-strand3997123
β-strand4002123
β-strand4008-4009224
β-strand4015-4016224
α-helix4018-40247
α-helix4050-407526
α-helix4086-40949
β-strand4097-4099325
β-strand4112-4114325
β-strand4125125
β-strand4130-4131226
α-helix4134-41385
α-helix4143-415816
α-helix4168-418720
α-helix4191-420717
α-helix4223-424422
α-helix4256-426914
α-helix4273-429523
α-helix4326-43305
α-helix4332-434716
α-helix4352-43598
α-helix4364-437512
α-helix4376-43805
α-helix4381-43844
α-helix4394-440613
α-helix4413-442311
α-helix4441-445616
α-helix4460-44623
α-helix4463-44708
α-helix4472-44754
β-strand4479127
β-strand4503-4504228
β-strand4510-4511228
β-strand4556127
β-strand4557129
α-helix4576-459621
α-helix4598-46047
β-strand4605129
α-helix4612-463120
α-helix4635-465117
α-helix4671-470535
α-helix4713-47197
α-helix4722-47243
α-helix4745-47473
α-helix4749-475810
α-helix4761-47644
α-helix4766-47738
α-helix4775-47784
α-helix4779-47835
α-helix4784-479714
α-helix4809-48146
α-helix4819-483820
α-helix4840-48456
α-helix4855-48573
α-helix4878-490225
β-strand4911130
α-helix4925-49295
α-helix4930-49345
β-strand4937-4941526
β-strand4948-4951426
α-helix4953-49608
β-strand4968130
α-helix4987-499711
α-helix5005-501410
α-helix5018-503720
β-strand5045131
α-helix5046-50483
α-helix5049-50535
α-helix5063-50664
β-strand5071131
α-helix5072-50743
α-helix5075-509218
α-helix5103-51064
α-helix5111-512212
α-helix5126-514015
β-strand5157132
α-helix5160-51689
α-helix5176-51805
β-strand5186132
α-helix5187-51893
α-helix5190-520415

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase RNF213Aprotein5247Homo sapiensQ63HN8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8S24_1 E3 ubiquitin-protein ligase RNF213 (chains A)
MASWSHPQFEKGSAGSAAGSGAGWSHPQFEKENLYFQAMSMECPSCQHVSKEETPKFCSQ
CGERLPPAAPIADSENNNSTMASASEGEMECGQELKEEGGPCLFPGSDSWQENPEEPCSK
ASWTVQESKKKKRKKKKKGNKSASSELASLPLSPASPCHLTLLSNPWPQDTALPHSQAQQ
SGPTGQPSQPPGTATTPLEGDGLSAPTEVGDSPLQAQALGEAGVATGSEAQSSPQFQDHT
EGEDQDASIPSGGRGLSQEGTGPPTSAGEGHSRTEDAAQELLLPESKGGSSEPGTELQTT
EQQAGASASMAVDAVAEPANAVKGAGKEMKEKTQRMKQPPATTPPFKTHCQEAETKTKDE
MAAAEEKVGKNEQGEPEDLKKPEGKNRSAAAVKNEKEQKNQEADVQEVKASTLSPGGGVT
VFFHAIISLHFPFNPDLHKVFIRGGEEFGESKWDSNICELHYTRDLGHDRVLVEGIVCIS
KKHLDKYIPYKYVIYNGESFEYEFIYKHQQKKGEYVNRCLFIKSSLLGSGDWHQYYDIVY
MKPHGRLQKVMNHITDGPRKDLVKGKQIAAALMLDSTFSILQTWDTINLNSFFTQFEQFC
FVLQQPMIYEGQAQLWTDLQYREKEVKRYLWQHLKKHVVPLPDGKSTDFLPVDCPVRSKL
KTGLIVLFVVEKIELLLEGSLDWLCHLLTSDASSPDEFHRDLSHILGIPQSWRLYLVNLC
QRCMDTRTYTWLGALPVLHCCMELAPRHKDAWRQPEDTWAALEGLSFSPFREQMLDTSSL
LQFMREKQHLLSIDEPLFRSWFSLLPLSHLVMYMENFIEHLGRFPAHILDCLSGIYYRLP
GLEQVLNTQDVQDVQNVQNILEMLLRLLDTYRDKIPEEALSPSYLTVCLKLHEAICSSTK
LLKFYELPALSAEIVCRMIRLLSLVDSAGQRDETGNNSVQTVFQGTLAATKRWLREVFTK
NMLTSSGASFTYVKEIEVWRRLVEIQFPAEHGWKESLLGDMEWRLTKEEPLSQITAYCNS
CWDTKGLEDSVAKTFEKCIIEAVSSACQSQTSILQGFSYSDLRKFGIVLSAVITKSWPRT
ADNFDDILKHLLTLADVKHVFRLCGTDEKILANVTEDAKRLIAVADSVLTKVVGDLLSGT
ILVGQLELIIKHKNQFLDIWQLREKSLSPQDEQCAVEEALDWRREELLLLKKEKRCVDSL
LKMCGNVKHLIQVDFGVLAVRHSQDLSSKRLNDTVTVRLSTSSNSQRATHYHLSSQVQEM
AGKIDLLRDSHIFQLFWREAAEPLSEPKEDQEAAELLSEPEEESERHILELEEVYDYLYQ
PSYRKFIKLHQDLKSGEVTLAEIDVIFKDFVNKYTDLDSELKIMCTVDHQDQRDWIKDRV
EQIKEYHHLHQAVHAAKVILQVKESLGLNGDFSVLNTLLNFTDNFDDFRRETLDQINQEL
IQAKKLLQDISEARCKGLQALSLRKEFICWVREALGGINELKVFVDLASISAGENDIDVD
RVACFHDAVQGYASLLFKLDPSVDFSAFMKHLKKLWKALDKDQYLPRKLCDSARNLEWLK
TVNESHGSVERSSLTLATAINQRGIYVIQAPKGGQKISPDTVLHLILPESPGSHEESREY
SLEEVKELLNKLMLMSGKKDRNNTEVERFSEVFCSVQRLSQAFIDLHSAGNMLFRTWIAM
AYCSPKQGVSLQMDFGLDLVTELKEGGDVTELLAALCRQMEHFLDSWKRFVTQKRMEHFY
LNFYTAEQLVYLSTELRKQPPSDAALTMLSFIKSNCTLRDVLRASVGCGSEAARYRMRRV
MEELPLMLLSEFSLVDKLRIIMEQSMRCLPAFLPDCLDLETLGHCLAHLAGMGGSPVERC
LPRGLQVGQPNLVVCGHSEVLPAALAVYMQTPSQPLPTYDEVLLCTPATTFEEVALLLRR
CLTLGSLGHKVYSLLFADQLSYEVARQAEELFHNLCTQQHREDYQLVMVCDGDWEHCYLP
SAFSQHKVFVTPQAPLEAIQAYLAGHYRVPKQTLSAAAVFNDRLCVGIVASERAGVGKSL
YVKRLHDKMKMQLNVKNVPLKTIRLIDPQVDESRVLGALLPFLDAQYQKVPVLFHLDVTS
SVQTGIWVFLFKLLILQYLMDINGKMWLRNPCHLYIVEILERRTSVPSRSSSALRTRVPQ
FSFLDIFPKVTCRPPKEVIDMELSALRSDTEPGMDLWEFCSETFQRPYQYLRRFNQNQDL
DTFQYQEGSVEGTPEECLQHFLFHCGVINPSWSELRNFARFLNYQLRDCEASLFCNPSFI
GDTLRGFKKFVVTFMIFMARDFATPSLHTSDQSPGKHMVTMDGVREEDLAPFSLRKRWES
EPHPYVFFNDDHTTMTFIGFHLQPNINGSVDAISHLTGKVIKRDVMTRDLYQGLLLQRVP
FNVDFDKLPRHKKLERLCLTLGIPQATDPDKTYELTTDNMLKILAIEMRFRCGIPVIIMG
ETGCGKTRLIKFLSDLRRGGTNADTIKLVKVHGGTTADMIYSRVREAENVAFANKDQHQL
DTILFFDEANTTEAISCIKEVLCDHMVDGQPLAEDSGLHIIAACNPYRKHSEEMICRLES
AGLGYRVSMEETADRLGSIPLRQLVYRVHALPPSLIPLVWDFGQLSDVAEKLYIQQIVQR
LVESISLDENGTRVITEVLCASQGFMRKTEDECSFVSLRDVERCVKVFRWFHEHSAMLLA
QLNAFLSKSSVSKNHTERDPVLWSLMLAIGVCYHASLEKKDSYRKAIARFFPKPYDDSRL
LLDEITRAQDLFLDGVPLRKTIAKNLALKENVFMMVVCIELKIPLFLVGKPGSSKSLAKT
IVADAMQGPAAYSDLFRSLKQVHLVSFQCSPHSTPQGIISTFRQCARFQQGKDLQQYVSV
VVLDEVGLAEDSPKMPLKTLHPLLEDGCIEDDPAPHKKVGFVGISNWALDPAKMNRGIFV
SRGSPNETELIESAKGICSSDILVQDRVQGYFASFAKAYETVCKRQDKEFFGLRDYYSLI
KMVFAAAKASNRKPSPQDIAQAVLRNFSGKDDIQALDIFLANLPEAKCSEEVSPMQLIKQ
NIFGPSQKVPGGEQEDAESRYLLVLTKNYVALQILQQTFFEGDQQPEIIFGSGFPKDQEY
TQLCRNINRVKICMETGKMVLLLNLQNLYESLYDALNQYYVHLGGQKYVDLGLGTHRVKC
RVHPNFRLIVIEEKDVVYKHFPIPLINRLEKHYLDINTVLEKWQKSIVEELCAWVEKFIN
VKAHHFQKRHKYSPSDVFIGYHSDACASVVLQVIERQGPRALTEELHQKVSEEAKSILLN
CATPDAVVRLSAYSLGGFAAEWLSQEYFHRQRHNSFADFLQAHLHTADLERHAIFTEITT
FSRLLTSHDCEILESEVTGRAPKPTLLWLQQFDTEYSFLKEVRNCLTNTAKCKILIFQTD
FEDGIRSAQLIASAKYSVINEINKIRENEDRIFVYFITKLSRVGRGTAYVGFHGGLWQSV
HIDDLRRSTLMVSDVTRLQHVTISQLFAPGDLPELGLEHRAEDGHEEAMETEASTSGEVA
EVAEEAMETESSEKVGKETSELGGSDVSILDTTRLLRSCVQSAVGMLRDQNESCTRNMRR
VVLLLGLLNEDDACHASFLRVSKMRLSVFLKKQEESQFHPLEWLAREACNQDALQEAGTF
RHTLWKRVQGAVTPLLASMISFIDRDGNLELLTRPDTPPWARDLWMFIFSDTMLLNIPLV
MNNERHKGEMAYIVVQNHMNLSENASNNVPFSWKIKDYLEELWVQAQYITDAEGLPKKFV
DIFQQTPLGRFLAQLHGEPQQELLQCYLKDFILLTMRVSTEEELKFLQMALWSCTRKLKA
ASEAPEEEVSLPWVHLAYQRFRSRLQNFSRILTIYPQVLHSLMEARWNHELAGCEMTLDA
FAAMACTEMLTRNTLKPSPQAWLQLVKNLSMPLELICSDEHMQGSGSLAQAVIREVRAQW
SRIFSTALFVEHVLLGTESRVPELQGLVTEHVFLLDKCLRENSDVKTHGPFEAVMRTLCE
CKETASKTLSRFGIQPCSICLGDAKDPVCLPCDHVHCLRCLRAWFASEQMICPYCLTALP
DEFSPAVSQAHREAIEKHARFRQMCNSFFVDLVSTICFKDNAPPEKEVIESLLSLLFVQK
GRLRDAAQRHCEHTKSLSPFNDVVDKTPVIRSVILKLLLKYSFHDVKDYIQEYLTLLKKK
AFITEDKTELYMLFINCLEDSILEKTSAYSRNDELNHLEEEGRFLKAYSPASRGREPANE
ASVEYLQEVARIRLCLDRAADFLSEPEGGPEMAKEKQCYLQQVKQFCIRVENDWHRVYLV
RKLSSQRGMEFVQGLSKPGRPHQWVFPKDVVKQQGLRQDHPGQMDRYLVYGDEYKALRDA
VAKAVLECKPLGIKTALKACKTPQSQQSAYFLLTLFREVAILYRSHNASLHPTPEQCEAV
SKFIGECKILSPPDISRFATSLVDNSVPLLRAGPSDSNLDGTVTEMAIHAAAVLLCGQNE
LLEPLKNLAFSPATMAHAFLPTMPEDLLAQARRWKGLERVHWYTCPNGHPCSVGECGRPM
EQSICIDCHAPIGGIDHKPRDGFHLVKDKADRTQTGHVLGNPQRRDVVTCDRGLPPVVFL
LIRLLTHLALLLGASQSSQALINIIKPPVRDPKGFLQQHILKDLEQLAKMLGHSADETIG
VVHLVLRRLLQEQHQLSSRRLLNFDTELSTKEMRNNWEKEIAAVISPELEHLDKTLPTMN
NLISQDKRISSNPVAKIIYGDPVTFLPHLPRKSVVHCSKIWSCRKRITVEYLQHIVEQKN
GKERVPILWHFLQKEAELRLVKFLPEILALQRDLVKQFQNVQQVEYSSIRGFLSKHSSDG
LRQLLHNRITVFLSTWNKLRRSLETNGEINLPKDYCSTDLDLDTEFEILLPRRRGLGLCA
TALVSYLIRLHNEIVYAVEKLSKENNSYSVDAAEVTELHVISYEVERDLTPLILSNCQYQ
VEEGRETVQEFDLEKIQRQI

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
MGMagnesium ionMg1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31

Primary citation

Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213. Crespillo-Casado, A., Pothukuchi, P., Naydenova, K. et al. EMBO Rep (2024) 25:4979-5005. DOI 10.1038/s44319-024-00280-w · PubMed

Other PDB entries of the same protein (UniProt Q63HN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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