9G09: Human RNF213

Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri. Determined by electron microscopy at 3.4 Å resolution. Released 16 Apr 2025.

Method
Electron microscopy
Resolution
3.4 Å
Organisms
Shigella flexneri 5a str. M90T, Homo sapiens
Chains
2
Atoms
38,435
Mol. weight
660.83 kDa
Ligands
ZN, MG, ATP
Released
16 Apr 2025

Explore 9G09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9G09 contains 282 α-helices and 112 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: 274 helices, 100 β-strands

ElementResiduesLengthSheet
β-strand379-38794
β-strand399-40465
β-strand418-42035
β-strand421-42224
β-strand431-43994
α-helix441-4433
β-strand447-45595
β-strand460-46235
β-strand463-46426
β-strand477-48155
β-strand491-49994
β-strand500-50126
α-helix518-54023
α-helix546-56419
β-strand567-57045
β-strand572-57545
α-helix584-59815
α-helix619-63214
α-helix642-6476
α-helix655-66612
α-helix672-68514
α-helix690-6934
α-helix695-7028
α-helix704-7063
α-helix711-7133
α-helix716-7194
α-helix727-7337
α-helix737-74610
α-helix750-7534
α-helix757-7648
α-helix767-77610
α-helix778-7836
α-helix787-80721
α-helix811-83020
α-helix843-85816
α-helix862-8643
α-helix866-88015
α-helix899-91719
β-strand92317
β-strand93017
α-helix935-9439
α-helix949-9513
α-helix953-96614
α-helix970-97910
α-helix983-9853
α-helix990-100920
α-helix1022-103615
α-helix1044-105310
α-helix1056-106611
α-helix1069-10735
α-helix1076-109823
β-strand110218
α-helix1103-11119
α-helix1113-112614
α-helix1135-116632
α-helix1167-11693
β-strand117319
α-helix1176-11838
α-helix1186-11883
β-strand119018
α-helix1191-11944
β-strand1195110
α-helix1205-12073
β-strand1209110
α-helix1215-122612
α-helix1231-12344
β-strand126919
α-helix1271-12744
α-helix1275-12795
α-helix1280-129516
α-helix1300-13067
α-helix1314-132512
α-helix1336-136227
α-helix1363-13675
α-helix1373-13753
α-helix1376-13838
α-helix1385-13884
α-helix1399-14068
α-helix1412-142211
α-helix1425-143410
α-helix1438-145114
α-helix1456-147116
α-helix14731
α-helix1474-14785
α-helix1485-150117
α-helix1505-151410
α-helix1516-15249
α-helix1533-154210
β-strand1545-1548411
α-helix1550-15512
α-helix1555-15573
α-helix1559-15624
β-strand1563-1567511
β-strand1578-1581411
α-helix1582-159514
α-helix1603-162927
α-helix1633-16353
β-strand1638-1646911
β-strand1649-1654611
β-strand1663-1665311
α-helix1669-169729
α-helix1700-17034
α-helix1706-171611
α-helix1721-17222
α-helix1723-17308
α-helix1738-17458
α-helix1751-177020
α-helix1774-178714
α-helix1799-181214
α-helix1816-18172
α-helix1821-18222
β-strand1830-1835612
α-helix1837-184913
α-helix1855-18562
β-strand1862-1864312
α-helix1871-188212
β-strand1892-1895412
α-helix1897-18993
α-helix1902-191716
β-strand1926-1931612
α-helix1932-19343
α-helix1938-19425
α-helix1944-19463
β-strand1947112
α-helix1956-196712
β-strand1968113
α-helix1969-19702
α-helix1976-19794
β-strand1984113
β-strand1986-1991614
α-helix1998-201215
β-strand2020-2025614
β-strand2029115
α-helix2032-20398
α-helix2040-20434
α-helix2045-20495
β-strand2052-2058714
β-strand2064115
α-helix2066-20705
α-helix2071-20755
β-strand2078-2080316
β-strand2086-2088316
β-strand2093-2100814
α-helix2123-21264
β-strand2129-2131314
α-helix2135-21417
α-helix2156-21594
α-helix2162-217514
α-helix2185-21862
α-helix2194-220512
α-helix2212-223120
α-helix2247-226317
β-strand2305-2308417
β-strand2315-2318417
β-strand2321-2324418
β-strand2329-2333518
β-strand2340-2347818
α-helix2348-23569
α-helix2365-23673
α-helix2370-238112
α-helix2397-241216
β-strand2416-2419419
α-helix2426-243813
β-strand2446-2450519
α-helix2457-247721
β-strand2482-2487619
α-helix2489-24913
α-helix2495-24995
α-helix2500-25045
β-strand2506-2507220
β-strand2510-2511220
α-helix25121
β-strand2518-2524719
β-strand2529121
α-helix2532-25409
β-strand2555-2556222
β-strand2559-2560222
α-helix2561-25633
β-strand2564121
α-helix2569-25724
β-strand2580-2581219
α-helix2587-260519
α-helix2609-262820
α-helix2639-266830
α-helix2680-268910
α-helix2690-26945
α-helix2700-27089
α-helix27121
α-helix2718-273316
α-helix2746-276116
β-strand2765-2768423
α-helix2775-278511
α-helix2794-27985
β-strand2801-2808823
α-helix2815-282915
β-strand2837-2844823
α-helix2846-28494
α-helix2856-28594
α-helix2860-28656
α-helix2872-28732
α-helix2875-28773
β-strand2880-2885623
α-helix2891-28944
β-strand2898-2901423
α-helix2902-29054
α-helix2907-291812
α-helix2923-294523
α-helix2953-297018
α-helix2973-29753
α-helix2976-298712
α-helix2995-30017
α-helix3004-30074
α-helix3014-30229
α-helix3038-30414
β-strand3042-3046524
α-helix3051-30588
β-strand3067-3069324
α-helix3080-309617
β-strand3100-3102324
α-helix3106-31083
α-helix3109-31179
β-strand3121-3123325
β-strand3126-3133825
β-strand3136-3142725
β-strand3148-3153624
α-helix3154-31596
α-helix3163-31686
β-strand3170-3173424
α-helix3176-31794
α-helix3182-320019
α-helix3214-32174
β-strand3218126
α-helix3225-323713
α-helix3240-32423
α-helix3244-326017
β-strand3262126
α-helix3264-327411
α-helix3278-328811
α-helix3296-330611
β-strand3313-3320827
α-helix3323-33253
α-helix3327-333711
α-helix3343-33442
β-strand3345-3348427
α-helix3349-33513
α-helix3355-336612
β-strand3372-3380927
α-helix3388-340417
β-strand3411-3419927
β-strand3439-3441327
α-helix3453-34542
α-helix3458-34603
α-helix3463-34664
α-helix3532-354615
β-strand3547-3549328
α-helix3556-356712
α-helix3573-359422
α-helix3600-36023
α-helix3603-36086
α-helix3611-36177
α-helix3620-364324
α-helix3649-36535
α-helix3659-367012
β-strand3693-3695328
α-helix3712-372918
β-strand3731129
β-strand3734129
α-helix3735-374511
α-helix3747-37548
α-helix3758-377518
α-helix3781-380020
α-helix3812-38209
α-helix3822-383413
α-helix3838-38425
α-helix3858-387114
α-helix3879-389618
α-helix3907-392923
α-helix3930-39345
α-helix3935-39406
α-helix3942-39443
α-helix3945-395915
α-helix3968-398922
β-strand4007-4008230
β-strand4016-4017230
α-helix4018-40247
α-helix4049-407123
α-helix4072-40776
α-helix4083-40853
α-helix4086-409510
β-strand4097-4098231
β-strand4113-4114231
β-strand4130-4131232
α-helix4133-41397
α-helix4143-415715
α-helix4168-418619
α-helix4191-420717
α-helix4223-424422
α-helix4254-427017
α-helix4274-428613
α-helix4289-42968
α-helix4303-43053
α-helix4308-43136
α-helix4326-43305
α-helix4332-434716
α-helix4352-43598
α-helix4364-437512
α-helix4376-43805
α-helix4381-43833
α-helix4388-43903
α-helix4392-43932
α-helix4394-440613
α-helix4413-442311
α-helix4441-445616
α-helix4460-44623
α-helix4463-44708
α-helix4472-44776
β-strand4479133
α-helix4487-44915
β-strand4503-4504234
β-strand4510-4511234
β-strand4556133
β-strand4557135
α-helix4562-45643
α-helix4576-459621
α-helix4598-46047
β-strand4605135
α-helix4612-463120
α-helix4635-465117
α-helix4671-468919
α-helix4692-470413
α-helix4707-47104
α-helix4713-47197
α-helix4722-47243
α-helix4734-47363
α-helix4745-47473
α-helix4749-475810
α-helix4761-47644
α-helix4766-477813
α-helix4779-47835
α-helix4784-479815
α-helix4809-48157
α-helix4819-484325
α-helix4853-48575
α-helix4866-48694
α-helix4877-490226
α-helix4925-49295
α-helix4930-49367
β-strand4937-4942632
β-strand4945-4951732
α-helix4953-496412
α-helix4982-49843
α-helix4987-499711
α-helix5002-50043
α-helix5005-501410
α-helix5018-503720
β-strand5045136
α-helix5046-50483
α-helix5049-50535
α-helix5063-50675
β-strand5071136
α-helix5072-50743
α-helix5075-509218
α-helix5103-51053
α-helix5111-512212
α-helix5126-513611
α-helix5137-51415
α-helix51421
α-helix5144-51485
β-strand5157137
α-helix5158-516811
α-helix5171-51744
α-helix5175-51795
β-strand5186137
α-helix5190-520617
Chain B: 8 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix38-5013
α-helix58-7114
β-strand7711
α-helix88-903
β-strand95-9731
β-strand115-11731
α-helix128-1303
β-strand135-13731
β-strand14512
β-strand155-15731
β-strand16512
β-strand175-17733
α-helix188-1903
β-strand195-19733
α-helix207-2093
β-strand215-21733
α-helix229-2324
β-strand238-24033
α-helix248-25912
β-strand267-26933

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase IpaH2.5Bprotein563Shigella flexneri 5a str. M90TA0A0H2USC0 (AlphaFold model)
E3 ubiquitin-protein ligase RNF213Aprotein5247Homo sapiensQ63HN8 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>9G09_1 E3 ubiquitin-protein ligase IpaH2.5 (chains B)
MIKSTNIQVIGSGIMHQINNIHSLTLFSLPVSLSPSCNEYYLKVWSEWERNGTPGEQRNI
AFNRLKICLQNQEAELNLSELDLKTLPDLPPQITTLEIRKNLLTHLPDLPPMLKVIHAQF
NQLESLPALPETLEELNAGDNKIKELPFLPENLTHLRVHNNRLHILPLLPPELKLLVVSG
NRLDSIPPFPDKLEGLALANNFIEQLPELPFSMNRAVLMNNNLTTLPESVLRLAQNAFVN
VAGNPLSGHTMRTLQQITTGPDYSGPQIFFSMGNSATISAPEHSLADAVTAWFPENKQSD
VSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAV
AADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDK
VRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENE
FTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAERE
AGAQVMRETEQQIYRQLTDEVLA
Sequence of entity 2 (A), FASTA
>9G09_2 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
ADNFNDILKHLLTLADVKHVFRLCGTDEKILANVTEDAKRLIAVADSVLTKVVGDLLSGT
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 ionZn3
MGMagnesium ionMg1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31

Primary citation

Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213. Naydenova, K., Boyle, K.B., Pathe, C. et al. Nat Struct Mol Biol (2025) 32:1741-1751. DOI 10.1038/s41594-025-01530-8 · PubMed

Other PDB entries of the same protein (UniProt A0A0H2USC0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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