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- PDB-9g08: Structure of human RNF213 bound to the secreted effector IpaH1.4 ... -

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Basic information

Entry
Database: PDB / ID: 9g08
TitleStructure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri
Components
  • E3 ubiquitin-protein ligase IpaH1.4
  • E3 ubiquitin-protein ligase RNF213
KeywordsANTIMICROBIAL PROTEIN / RNF213 / IpaH1.4 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA ATPase
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination / immune system process / protein autoubiquitination / lipid droplet / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / toxin activity / ubiquitin-dependent protein catabolic process / angiogenesis / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / defense response to bacterium / protein ubiquitination / nucleolus / ATP hydrolysis activity / extracellular region / zinc ion binding / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine-rich repeats, bacterial type / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Leucine-rich repeat profile. / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / E3 ubiquitin-protein ligase IpaH1.4 / E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri 5a str. M90T (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsNaydenova, K. / Randow, F.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)U105170648 United Kingdom
Wellcome Trust222503/Z/21/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213.
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 /
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.
History
DepositionJul 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.3Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF213
B: E3 ubiquitin-protein ligase IpaH1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)662,1037
Polymers661,3752
Non-polymers7285
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein E3 ubiquitin-protein ligase RNF213 / ALK lymphoma oligomerization partner on chromosome 17 / E3 ubiquitin-lipopolysaccharide ligase ...ALK lymphoma oligomerization partner on chromosome 17 / E3 ubiquitin-lipopolysaccharide ligase RNF213 / Mysterin / RING finger protein 213


Mass: 596450.250 Da / Num. of mol.: 1 / Mutation: D1045N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF213, ALO17, C17orf27, KIAA1554, KIAA1618, MYSTR / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q63HN8, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; ...References: UniProt: Q63HN8, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein E3 ubiquitin-protein ligase IpaH1.4 / Invasion plasmid antigen 1.4


Mass: 64925.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 5a str. M90T (bacteria)
Gene: ipaH1.4, SF_p0265 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2USG1, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shigella flexneri
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.56 sec. / Electron dose: 32 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16931

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Processing

EM software
IDNameCategory
2EPUimage acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334921 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00639246
ELECTRON MICROSCOPYf_angle_d0.70153122
ELECTRON MICROSCOPYf_dihedral_angle_d40.9125150
ELECTRON MICROSCOPYf_chiral_restr0.0436004
ELECTRON MICROSCOPYf_plane_restr0.0066779

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