9JTA: RNF213 RING domain

Crystal structure of RNF213 RING domain bound to IpaH1.4 LRR domain. Determined by X-ray diffraction at 1.7 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Shigella flexneri 5a str. M90T, Homo sapiens
Chains: 2
Atoms: 2,533
Mol. weight: 34.23 kDa
Ligands: ZN
Released: 7 May 2025

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

Secondary structure: helices and β-sheets

9JTA contains 12 α-helices and 16 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 B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
α-helix	58-70	13
β-strand	75-77	3	1
α-helix	89-90	2
β-strand	95-97	3	1
α-helix	108-110	3
β-strand	115-117	3	1
α-helix	128-130	3
β-strand	135-137	3	1
α-helix	146-150	5
β-strand	155-157	3	1
α-helix	167-170	4
β-strand	175-177	3	1
α-helix	187-190	4
β-strand	195-197	3	1
α-helix	207-210	4
β-strand	215-217	3	1
α-helix	228-232	5
β-strand	238-240	3	1
α-helix	248-258	11
β-strand	267-269	3	1

Chain C: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3996	1	2
β-strand	4003	1	2
β-strand	4007-4009	3	3
β-strand	4015-4017	3	3
α-helix	4018-4025	8
β-strand	4031	1	4
β-strand	4038	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RING-type E3 ubiquitin transferase	B	protein	235	Shigella flexneri 5a str. M90T	A0A4P7TTK5 (AlphaFold model)
E3 ubiquitin-protein ligase RNF213	C	protein	67	Homo sapiens	Q63HN8 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9JTA_1 RING-type E3 ubiquitin transferase (chains B)
MNEFYLKTWSEWEKNGTPGEQRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPPQITTL
EIRKNLLTHLPDLPPMLKVIHAQFNQLESLPALPETLEELNAGDNKIKELPFLPENLTHL
RVHNNRLHILPLLPPELKLLVVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPFSMNRA
VLMNNNLTTLPESVLRLAQNAFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFS

Sequence of entity 2 (C), FASTA

>9JTA_2 E3 ubiquitin-protein ligase RNF213 (chains C)
SRFGIQPCSICLGDAKDPVCLPCDHVHCLRCLRAWFASEQMICPYCLTALPDEFSPAVSQ
AHREAIE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

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