Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213.
Journal, issue, pages	Nat Struct Mol Biol, Year 2025
Publish date	Apr 9, 2025
Authors	Katerina Naydenova / Keith B Boyle / Claudio Pathe / Prathyush Pothukuchi / Ana Crespillo-Casado / Felix Scharte / Pierre-Mehdi Hammoudi / Elsje G Otten / Neal M Alto / Felix Randow /
PubMed Abstract	Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates 'eat me' signals for ...Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates 'eat me' signals for antibacterial autophagy, but whether and how cytosol-adapted bacteria avoid LPS ubiquitylation remains poorly understood. Here, we show that the enterobacterium Shigella flexneri actively antagonizes LPS ubiquitylation through IpaH1.4, a secreted effector protein with ubiquitin E3 ligase activity. IpaH1.4 binds to RNF213, ubiquitylates it and targets it for proteasomal degradation, thus counteracting host-protective LPS ubiquitylation. To understand how IpaH1.4 recognizes RNF213, we determined the cryogenic electron microscopy structure of the IpaH1.4-RNF213 complex. The specificity of the interaction is achieved through the leucine-rich repeat of IpaH1.4, which binds the RING domain of RNF213 by hijacking the conserved RING interface required for binding to ubiquitin-charged E2 enzymes. IpaH1.4 also targets other E3 ligases involved in inflammation and immunity through binding to the E2-interacting face of their RING domains, including the E3 ligase LUBAC that is required for the synthesis of M1-linked ubiquitin chains on cytosol-invading bacteria downstream of RNF213. We conclude that IpaH1.4 has evolved to antagonize multiple antibacterial and proinflammatory host E3 ligases.
External links	Nat Struct Mol Biol / PubMed:40205224
Methods	EM (single particle)
Resolution	2.9 - 3.4 Å
Structure data	50913 9g08 EMDB-50913, PDB-9g08: Structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.3 Å 50914 9g09 EMDB-50914, PDB-9g09: Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.4 Å EMDB-50915: Consensus refinement of the complex between human RNF213 and the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.0 Å EMDB-50916: Local refinement of the RNF213 CBM domain in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.2 Å EMDB-50917: Local refinement of the RNF213 stalk domain in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.4 Å EMDB-50918: Local refinement of the RNF213 ATPase domain in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 2.9 Å EMDB-50919: Local refinement of the RNF213 C-terminal and hinge domains in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.1 Å EMDB-50920: Local refinement of the RNF213 E3 module in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.1 Å EMDB-50921: Local refinement of the RNF213 RING domain and the IpaH1.4 LRR domain in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri Method: EM (single particle) / Resolution: 3.3 Å EMDB-50922: Consensus refinement of the complex between human RNF213 and the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.2 Å EMDB-50923: Local refinement of the RNF213 CBM domain in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.1 Å EMDB-50924: Local refinement of the RNF213 stalk domain in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.3 Å EMDB-50925: Local refinement of the RNF213 ATPase domain in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.0 Å EMDB-50926: Local refinement of the RNF213 C-terminal and hinge domains in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.1 Å EMDB-50928: Local refinement of the RNF213 E3 module in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.1 Å EMDB-50929: Local refinement of the RNF213 RING domain and the IpaH2.5 LRR domain in the structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri Method: EM (single particle) / Resolution: 3.4 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-ZN*: Unknown entry
Source	homo sapiens (human) shigella flexneri 5a str. m90t (bacteria) Homo (humans)
Keywords	ANTIMICROBIAL PROTEIN / RNF213 / IpaH1.4 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA ATPase / IpaH2.5