SMTL ID : 9g09.1

Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain B: A.2034, G.2035, V.2036, G.2037, K.2038, S.2039, L.2040, E.2138, G.2193, M.2194, D.2195, E.2198, F.2204, W.2252, R.2256, K.2539, S.2614 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.2035, B:V.2036, B:G.2037, B:K.2038, B:S.2039, B:L.2040, B:G.2193, B:D.2195, B:E.2198, B:R.2256, B:S.2614 Salt bridges: B:K.2038, B:K.2038, B:K.2539, B:K.2539 pi-Stacking: B:W.2252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: S.2039, E.2138, D.2544 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.2039, B:E.2138

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain B: H.4549, C.4565, I.4566 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.4549, B:C.4565, B:I.4566 ZN.4: 6 residues within 4Å: Chain B: C.4037, I.4039, C.4040, K.4045, C.4057, C.4060 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.4040, B:C.4060 ZN.5: 4 residues within 4Å: Chain B: C.4052, H.4054, C.4072, C.4075 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.4054, B:C.4072, B:C.4075

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naydenova, K. et al., Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-04-16

Peptides

E3 ubiquitin-protein ligase IpaH2.5: A
E3 ubiquitin-protein ligase RNF213: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

E3 ubiquitin-protein ligase IpaH2.5

E3 ubiquitin-protein ligase RNF213

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