SMTL ID : 9g08.1

Structure of human RNF213 bound to the secreted effector IpaH1.4 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: 20 residues within 4Å: Chain A: A.2034, G.2035, V.2036, G.2037, K.2038, S.2039, L.2040, E.2138, L.2140, G.2193, M.2194, D.2195, E.2198, F.2204, W.2252, S.2253, R.2256, K.2539, S.2614 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.2035, A:V.2036, A:G.2037, A:K.2038, A:S.2039, A:S.2039, A:L.2040, A:G.2193, A:D.2195, A:E.2198, A:S.2614 Salt bridges: A:K.2038, A:K.2038, A:K.2539, A:K.2539 pi-Stacking: A:W.2252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: S.2039, R.2064, E.2138, K.2539, D.2544 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2039, A:E.2138

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.4549, P.4550, C.4551, C.4568, R.4913 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.4549, A:P.4550 ZN.4: 7 residues within 4Å: Chain A: C.4037, I.4039, C.4040, A.4044, K.4045, C.4057, C.4060 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4037, A:C.4040, A:C.4057, A:C.4060 ZN.5: 4 residues within 4Å: Chain A: C.4052, H.4054, C.4075, T.4077 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.4052, A:H.4054, A: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 RNF213: A
E3 ubiquitin-protein ligase IpaH1.4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase RNF213

E3 ubiquitin-protein ligase IpaH1.4

Related Entries With Identical Sequence