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- EMDB-50919: Local refinement of the RNF213 C-terminal and hinge domains in th... -

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Entry
Database: EMDB / ID: EMD-50919
TitleLocal 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
Map dataFocused refinement of the RNF213 C-terminal and hinge domains in the RNF213-IpaH1.4 complex (post-processed, auto-sharpened map)
Sample
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shigella flexneri
KeywordsRNF213 / IpaH1.4 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA / ATPase / ANTIMICROBIAL PROTEIN
Biological speciesHomo (humans)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNaydenova K / Randow F
Funding support United Kingdom, 2 items
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, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50919.png

Downloads & links

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Map

FileDownload / File: emd_50919.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of the RNF213 C-terminal and hinge domains in the RNF213-IpaH1.4 complex (post-processed, auto-sharpened map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 384 pix.
= 471.552 Å		1.23 Å/pix.
x 384 pix.
= 471.552 Å		1.23 Å/pix.
x 384 pix.
= 471.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.228 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.10502649 - 0.18286699
Average (Standard dev.)0.00002104491 (±0.001508603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 471.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50919_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of the RNF213 C-terminal and hinge...

Fileemd_50919_additional_1.map
AnnotationFocused refinement of the RNF213 C-terminal and hinge domains in the RNF213-IpaH1.4 complex (non-filtered, non-sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused refinement of the RNF213 C-terminal and hinge...

Fileemd_50919_half_map_1.map
AnnotationFocused refinement of the RNF213 C-terminal and hinge domains in the RNF213-IpaH1.4 complex (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused refinement of the RNF213 C-terminal and hinge...

Fileemd_50919_half_map_2.map
AnnotationFocused refinement of the RNF213 C-terminal and hinge domains in the RNF213-IpaH1.4 complex (half map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shi...

EntireName: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shigella flexneri
Components
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shigella flexneri

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Supramolecule #1: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shi...

SupramoleculeName: E3 ligase RNF213, bound to the secreted effector IpaH1.4 from Shigella flexneri
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo (humans)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 16931 / Average exposure time: 4.56 sec. / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 0.7000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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