[English] 日本語
Yorodumi
- EMDB-50920: Local refinement of the RNF213 E3 module in the structure of huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50920
TitleLocal refinement of the RNF213 E3 module in the structure of human RNF213 bound to the secreted effector IpaH1.4 from Shigella flexneri
Map dataFocused refinement of the RNF213 E3 module 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-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50920.png

Downloads & links

-
Map

FileDownload / File: emd_50920.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of the RNF213 E3 module 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: 0.04
Minimum - Maximum-0.10623052 - 0.18107186
Average (Standard dev.)0.00002139092 (±0.0017161652)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_50920_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused refinement of the RNF213 E3 module in...

Fileemd_50920_additional_1.map
AnnotationFocused refinement of the RNF213 E3 module in the RNF213-IpaH1.4 complex (non-filtered, non-sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused refinement of the RNF213 E3 module in...

Fileemd_50920_half_map_1.map
AnnotationFocused refinement of the RNF213 E3 module in the RNF213-IpaH1.4 complex (half map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused refinement of the RNF213 E3 module in...

Fileemd_50920_half_map_2.map
AnnotationFocused refinement of the RNF213 E3 module in the RNF213-IpaH1.4 complex (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more