9JWG: E3 ubiquitin-protein ligase IpaH1.4

Cryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4 LRR domain. Determined by electron microscopy at 3.47 Å resolution. Released 7 May 2025.

Method
Electron microscopy
Resolution
3.47 Å
Organisms
Shigella flexneri, Homo sapiens
Chains
2
Atoms
11,647
Mol. weight
618.94 kDa
Released
7 May 2025

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

Secondary structure: helices and β-sheets

9JWG contains 83 α-helices and 20 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: 72 helices, 10 β-strands

ElementResiduesLengthSheet
α-helix3712-372918
α-helix3732-37343
α-helix3735-374511
α-helix3747-37537
α-helix3759-377315
α-helix3781-380020
α-helix3811-382010
α-helix3822-383413
α-helix3837-38437
α-helix3858-387215
α-helix3880-389718
α-helix3899-39013
α-helix3907-392519
α-helix3927-39293
α-helix3930-39345
α-helix3937-39404
α-helix3944-396017
α-helix3968-398922
α-helix4022-40265
α-helix4049-407729
α-helix4083-40853
α-helix4086-40938
α-helix4094-40963
β-strand4129-413022
α-helix4133-41397
α-helix4147-415812
α-helix4171-418515
α-helix4194-420310
α-helix4223-424321
α-helix4253-427018
α-helix4275-428612
α-helix4289-42946
α-helix4311-43166
α-helix4326-43283
α-helix4332-434716
α-helix4351-43599
α-helix4364-437411
α-helix4375-43795
α-helix4380-43823
α-helix4388-43903
α-helix4392-43932
α-helix4394-440512
α-helix4413-442311
α-helix4442-445615
α-helix4460-44623
α-helix4463-44686
α-helix4502-45032
β-strand450413
α-helix45051
β-strand451013
β-strand455714
α-helix4576-459015
α-helix4593-45953
α-helix4598-46025
β-strand460514
α-helix4615-463117
α-helix4635-465016
α-helix4671-468515
α-helix4687-46893
α-helix4695-47039
α-helix4713-47175
α-helix4734-47363
α-helix4743-47475
α-helix4749-475810
α-helix4766-47727
α-helix4781-47833
α-helix4784-47874
α-helix4790-47978
α-helix4809-48157
α-helix4820-483718
α-helix4840-48467
α-helix4875-48773
α-helix4878-489821
β-strand4910-491125
α-helix4917-49193
α-helix4925-49295
α-helix4930-49367
β-strand4937-494046
β-strand4941-494222
β-strand4948-495146
α-helix4953-49619
β-strand4970-497125
Chain B: 11 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix39-5012
α-helix58-7114
β-strand75-7731
α-helix88-903
β-strand95-9731
α-helix108-1103
β-strand115-11731
α-helix128-1303
β-strand135-13731
α-helix148-1503
β-strand155-15731
α-helix167-1704
β-strand175-17731
α-helix187-1904
β-strand195-19731
α-helix207-2104
β-strand215-21731
α-helix228-2325
β-strand238-24031
α-helix248-25811
β-strand267-26931

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
E3 ubiquitin-protein ligase IpaH1.4Bprotein579Shigella flexneriA0A0H2USG1 (AlphaFold model)
Ring finger protein 213Aprotein4841Homo sapiensA0A0A0MTR7
Sequence of entity 1 (B), FASTA
>9JWG_1 E3 ubiquitin-protein ligase IpaH1.4 (chains B)
GPGSMIKSTNIQAIGSGIMHQINNVYSLTPLSLPMELTPSMNEFYLKTWSEWEKNGTPGE
QRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPPQITTLEIRKNLLTHLPDLPPMLKVI
HAQFNQLESLPALPETLEELNAGDNKIKELPFLPENLTHLRVHNNRLHILPLLPPELKLL
VVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPFSMNRAVLMNNNLTTLPESVLRLAQN
AFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFSMGNSATISAPEHSLADAVTAWFPEN
KQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQ
SFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDI
ARDKVRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSR
EENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDAD
AEREAGAQVMRETEQQIYRQLTDEVLALRLSENGSNHIA
Sequence of entity 2 (A), FASTA
>9JWG_2 Ring finger protein 213 (chains A)
GPGTSTLSPGGGVTVFFHAIISLHFPFNPDLHKVFIRGGEEFGESKWDSNICELHYTRDL
GHDRVLVEGIVCISKKHLDKYIPYKYVIYNGESFEYEFIYKHQQKKGEYVNRCLFIKSSL
LGSGDWHQYYDIVYMKPHGRLQKVMNHITDGPRKDLVKGKQIAAALMLDSTFSILQTWDT
INLNSFFTQFEQFCFVLQQPMIYEGQAQLWTDLQYREKEVKRYLWQHLKKHVVPLPDGKS
TDFLPVDCPVRSKLKTGLIVLFVVEKIELLLEGSLDWLCHLLTSDASSPDEFHRDLSHIL
GIPQSWRLYLVNLCQRCMDTRTYTWLGALPVLHCCMELAPRHKDAWRQPEDTWAALEGLS
FSPFREQMLDTSSLLQFMREKQHLLSIDEPLFRSWFSLLPLSHLVMYMENFIEHLGRFPA
HILDCLSGIYYRLPGLEQVLNTQDVQDVQNVQNILEMLLRLLDTYRDKIPEEALSPSYLT
VCLKLHEAICSSTKLLKFYELPALSAEIVCRMIRLLSLVDSAGQRDETGNNSVQTVFQGT
LAATKRWLREVFTKNMLTSSGASFTYVKEIEVWRRLVEIQFPAEHGWKESLLGDMEWRLT
KEEPLSQITAYCNSCWDTKGLEDSVAKTFEKCIIEAVSSACQSQTSILQGFSYSDLRKFG
IVLSAVITKSWPRTADNFDDILKHLLTLADVKHVFRLCGTDEKILANVTEDAKRLIAVAD
SVLTKVVGDLLSGTILVGQLELIIKHKNQFLDIWQLREKSLSPQDEQCAVEEALDWRREE
LLLLKKEKRCVDSLLKMCGNVKHLIQVDFGVLAVRHSQDLSSKRLNDTVTVRLSTSSNSQ
RATHYHLSSQVQEMAGKIDLLRDSHIFQLFWREAAEPLSEPKEDQEAAELLSEPEEESER
HILELEEVYDYLYQPSYRKFIKLHQDLKSGEVTLAEIDVIFKDFVNKYTDLDSELKIMCT
VDHQDQRDWIKDRVEQIKEYHHLHQAVHAAKVILQVKESLGLNGDFSVLNTLLNFTDNFD
DFRRETLDQINQELIQAKKLLQDISEARCKGLQALSLRKEFICWVREALGGINELKVFVD
LASISAGENDIDVDRVACFHDAVQGYASLLFKLDPSVDFSAFMKHLKKLWKALDKDQYLP
RKLCDSARNLEWLKTVNESHGSVERSSLTLATAINQRGIYVIQAPKGGQKISPDTVLHLI
LPESPGSHEESREYSLEEVKELLNKLMLMSGKKDRNNTEVERFSEVFCSVQRLSQAFIDL
HSAGNMLFRTWIAMAYCSPKQGVSLQMDFGLDLVTELKEGGDVTELLAALCRQMEHFLDS
WKRFVTQKRMEHFYLNFYTAEQLVYLSTELRKQPPSDAALTMLSFIKSNCTLRDVLRASV
GCGSEAARYRMRRVMEELPLMLLSEFSLVDKLRIIMEQSMRCLPAFLPDCLDLETLGHCL
AHLAGMGGSPVERCLPRGLQVGQPNLVVCGHSEVLPAALAVYMQTPSQPLPTYDEVLLCT
PATTFEEVALLLRRCLTLGSLGHKVYSLLFADQLSYEVARQAEELFHNLCTQQHREDYQL
VMVCDGDWEHCYLPSAFSQHKVFVTPQAPLEAIQAYLAGHYRVPKQTLSAAAVFNDRLCV
GIVASERAGVGKSLYVKRLHDKMKMQLNVKNVPLKTIRLIDPQVDESRVLGALLPFLDAQ
YQKVPVLFHLDVTSSVQTGIWVFLFKLLILQYLMDINGKMWLRNPCHLYIVEILERRTSV
PSRSSSALRTRVPQFSFLDIFPKVTCRPPKEVIDMELSALRSDTEPGMDLWEFCSETFQR
PYQYLRRFNQNQDLDTFQYQEGSVEGTPEECLQHFLFHCGVINPSWSELRNFARFLNYQL
RDCEASLFCNPSFIGDTLRGFKKFVVTFMIFMARDFATPSLHTSDQSPGKHMVTMDGVRE
EDLAPFSLRKRWESEPHPYVFFNDDHTTMTFIGFHLQPNINGSVDAISHLTGKVIKRDVM
TRDLYQGLLLQRVPFNVDFDKLPRHKKLERLCLTLGIPQATDPDKTYELTTDNMLKILAI
EMRFRCGIPVIIMGETGCGKTRLIKFLSDLRRGGTNADTIKLVKVHGGTTADMIYSRVRE
AENVAFANKDQHQLDTILFFDEANTTEAISCIKEVLCDHMVDGQPLAEDSGLHIIAACNP
YRKHSEEMICRLESAGLGYRVSMEETADRLGSIPLRQLVYRVHALPPSLIPLVWDFGQLS
DVAEKLYIQQIVQRLVESISLDENGTRVITEVLCASQGFMRKTEDECSFVSLRDVERCVK
VFRWFHEHSAMLLAQLNAFLSKSSVSKNHTERDPVLWSLMLAIGVCYHASLEKKDSYRKA
IARFFPKPYDDSRLLLDEITRAQDLFLDGVPLRKTIAKNLALKENVFMMVVCIELKIPLF
LVGKPGSSKSLAKTIVADAMQGPAAYSDLFRSLKQVHLVSFQCSPHSTPQGIISTFRQCA
RFQQGKDLQQYVSVVVLDEVGLAEDSPKMPLKTLHPLLEDGCIEDDPAPHKKVGFVGISN
WALDPAKMNRGIFVSRGSPNETELIESAKGICSSDILVQDRVQGYFASFAKAYETVCKRQ
DKEFFGLRDYYSLIKMVFAAAKASNRKPSPQDIAQAVLRNFSGKDDIQALDIFLANLPEA
KCSEEVSPMQLIKQNIFGPSQKVPGGEQEDAESRYLLVLTKNYVALQILQQTFFEGDQQP
EIIFGSGFPKDQEYTQLCRNINRVKICMETGKMVLLLNLQNLYESLYDALNQYYVHLGGQ
KYVDLGLGTHRVKCRVHPNFRLIVIEEKDVVYKHFPIPLINRLEKHYLDINTVLEKWQKS
IVEELCAWVEKFINVKAHHFQKRHKYSPSDVFIGYHSDACASVVLQVIERQGPRALTEEL
HQKVSEEAKSILLNCATPDAVVRLSAYSLGGFAAEWLSQEYFHRQRHNSFADFLQAHLHT
ADLERHAIFTEITTFSRLLTSHDCEILESEVTGRAPKPTLLWLQQFDTEYSFLKEVRNCL
TNTAKCKILIFQTDFEDGIRSAQLIASAKYSVINEINKIRENEDRIFVYFITKLSRVGRG
TAYVGFHGGLWQSVHIDDLRRSTLMVSDVTRLQHVTISQLFAPGDLPELGLEHRAEDGHE
EAMETEASTSGEVAEVAEEAMETESSEKVGKETSELGGSDVSILDTTRLLRSCVQSAVGM
LRDQNESCTRNMRRVVLLLGLLNEDDACHASFLRVSKMRLSVFLKKQEESQFHPLEWLAR
EACNQDALQEAGTFRHTLWKRVQGAVTPLLASMISFIDRDGNLELLTRPDTPPWARDLWM
FIFSDTMLLNIPLVMNNERHKGEMAYIVVQNHMNLSENASNNVPFSWKIKDYLEELWVQA
QYITDAEGLPKKFVDIFQQTPLGRFLAQLHGEPQQELLQCYLKDFILLTMRVSTEEELKF
LQMALWSCTRKLKAASEAPEEEVSLPWVHLAYQRFRSRLQNFSRILTIYPQVLHSLMEAR
WNHELAGCEMTLDAFAAMACTEMLTRNTLKPSPQAWLQLVKNLSMPLELICSDEHMQGSG
SLAQAVIREVRAQWSRIFSTALFVEHVLLGTESRVPELQGLVTEHVFLLDKCLRENSDVK
THGPFEAVMRTLCECKETASKTLSRFGIQPCSICLGDAKDPVCLPCDHVHCLRCLRAWFA
SEQMICPYCLTALPDEFSPAVSQAHREAIEKHARFRQMCNSFFVDLVSTICFKDNAPPEK
EVIESLLSLLFVQKGRLRDAAQRHCEHTKSLSPFNDVVDKTPVIRSVILKLLLKYSFHDV
KDYIQEYLTLLKKKAFITEDKTELYMLFINCLEDSILEKTSAYSRNDELNHLEEEGRFLK
AYSPASRGREPANEASVEYLQEVARIRLCLDRAADFLSEPEGGPEMAKEKQCYLQQVKQF
CIRVENDWHRVYLVRKLSSQRGMEFVQGLSKPGRPHQWVFPKDVVKQQGLRQDHPGQMDR
YLVYGDEYKALRDAVAKAVLECKPLGIKTALKACKTPQSQQSAYFLLTLFREVAILYRSH
NASLHPTPEQCEAVSKFIGECKILSPPDISRFATSLVDNSVPLLRAGPSDSNLDGTVTEM
AIHAAAVLLCGQNELLEPLKNLAFSPATMAHAFLPTMPEDLLAQARRWKGLERVHWYTCP
NGHPCSVGECGRPMEQSICIDCHAPIGGIDHKPRDGFHLVKDKADRTQTGHVLGNPQRRD
VVTCDRGLPPVVFLLIRLLTHLALLLGASQSSQALINIIKPPVRDPKGFLQQHILKDLEQ
LAKMLGHSADETIGVVHLVLRRLLQEQHQLSSRRLLNFDTELSTKEMRNNWEKEIAAVIS
PELEHLDKTLPTMNNLISQDKRISSNPVAKIIYGDPVTFLPHLPRKSVVHCSKIWSCRKR
ITVEYLQHIVEQKNGKERVPILWHFLQKEAELRLVKFLPEILALQRDLVKQFQNVQQVEY
SSIRGFLSKHSSDGLRQLLHNRITVFLSTWNKLRRSLETNGEINLPKDYCSTDLDLDTEF
EILLPRRRGLGLCATALVSYLIRLHNEIVYAVEKLSKENNSYSVDAAEVTELHVISYEVE
RDLTPLILSNCQYQVEEGRETVQEFDLEKIQRQIVSRFLQGKPRLSLKGIPTLVYRHDWN
YEHLFMDIKNKMAQDSLPSSVISAISGQLQSYSDACEVLSVVEVTLGFLSTAGGDPNMQL
NVYTQDILQMGDQTIHVLKALNRCQLKHTIALWQFLSAHKSEQLLRLHKEPFGEISSRYK
ADLSPENAKLLSTFLNQTGLDAFLLELHEMIILKLKNPQTQTEERFRPQWSLRDTLVSYM
QTKESEILPEMASQFPEEILLASCVSVWKTAAVLKWNREMR

Primary citation

Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity. Zhou, X., Zhang, H., Wang, Y. et al. Nat Commun (2025) 16:3099-3099. DOI 10.1038/s41467-025-58432-y · PubMed

Other PDB entries of the same protein (UniProt A0A0H2USG1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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