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- PDB-9jwg: Cryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4... -

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Basic information

Entry
Database: PDB / ID: 9jwg
TitleCryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4 LRR domain
Components
  • E3 ubiquitin-protein ligase IpaH1.4
  • Ring finger protein 213
KeywordsCYTOSOLIC PROTEIN / RNF213 / IpaH1.4
Function / homology
Function and homology information


lipid ubiquitination / immune system process / lipid droplet / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / toxin activity / angiogenesis / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm ...lipid ubiquitination / immune system process / lipid droplet / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / toxin activity / 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 / 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
E3 ubiquitin-protein ligase RNF213 / E3 ubiquitin-protein ligase IpaH1.4
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Nat Commun / Year: 2025
Title: Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity.
Authors: Xindi Zhou / Huijing Zhang / Yaru Wang / Danni Wang / Zhiqiao Lin / Yuchao Zhang / Yubin Tang / Jianping Liu / Yu-Feng Yao / Yixiao Zhang / Lifeng Pan /
Abstract: Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial ...Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial immunity in mammals. Shigella flexneri, an LPS-containing pathogenic bacterium, has developed mechanisms to evade host antibacterial defenses during infection. However, the precise strategies by which S. flexneri circumvents RNF213-mediated antibacterial immunity remain poorly understood. Here, through comprehensive biochemical, structural and cellular analyses, we reveal that the E3 effector IpaH1.4 of S. flexneri can directly target human RNF213 via a specific interaction between the IpaH1.4 LRR domain and the RING domain of RNF213, and mediate the ubiquitination and proteasomal degradation of RNF213 in cells. Furthermore, we determine the cryo-EM structure of human RNF213 and the crystal structure of the IpaH1.4 LRR/RNF213 RING complex, elucidating the molecular mechanism underlying the specific recognition of RNF213 by IpaH1.4. Finally, our cell based functional assays demonstrate that the targeting of host RNF213 by IpaH1.4 promotes S. flexneri proliferation within infected cells. In summary, our work uncovers an unprecedented strategy employed by S. flexneri to subvert the key host immune factor RNF213, thereby facilitating bacterial proliferation during invasion.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase IpaH1.4
A: Ring finger protein 213


Theoretical massNumber of molelcules
Total (without water)618,9392
Polymers618,9392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein E3 ubiquitin-protein ligase IpaH1.4 / Invasion plasmid antigen 1.4


Mass: 65280.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH1.4, SF_p0265 / Production host: Homo sapiens (human)
References: UniProt: A0A0H2USG1, RING-type E3 ubiquitin transferase
#2: Protein Ring finger protein 213 / E3 ubiquitin-protein ligase RNF213


Mass: 553658.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF213 / Production host: Homo sapiens (human) / References: UniProt: A0A0A0MTR7
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: Human RNF213 and Shigella flexneri IpaH1.4 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.618 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Shigella flexneri (bacteria)623
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137886 / Symmetry type: POINT

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