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- PDB-8s24: Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM -

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Basic information

Entry
Database: PDB / ID: 8s24
TitleStructure of the E3 ubiquitin ligase RNF213, determined by cryoEM
ComponentsE3 ubiquitin-protein ligase RNF213
KeywordsANTIMICROBIAL PROTEIN / E3 ubiquitin ligase / ATPase / carbohydrate-binding domain / RING domain / RZ domain
Function / homology
Function and homology information


lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process ...lipid ubiquitination / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / Transferases; Acyltransferases; Aminoacyltransferases / sprouting angiogenesis / immune system process / protein K63-linked ubiquitination / regulation of lipid metabolic process / protein autoubiquitination / lipid droplet / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / angiogenesis / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ring finger / 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 RNF213
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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: EMBO Rep / Year: 2024
Title: Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213.
Authors: Ana Crespillo-Casado / Prathyush Pothukuchi / Katerina Naydenova / Matthew C J Yip / Janet M Young / Jerome Boulanger / Vimisha Dharamdasani / Ceara Harper / Pierre-Mehdi Hammoudi / Elsje G ...Authors: Ana Crespillo-Casado / Prathyush Pothukuchi / Katerina Naydenova / Matthew C J Yip / Janet M Young / Jerome Boulanger / Vimisha Dharamdasani / Ceara Harper / Pierre-Mehdi Hammoudi / Elsje G Otten / Keith Boyle / Mayuri Gogoi / Harmit S Malik / Felix Randow /
Abstract: Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition ...Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negative Salmonella, Gram-positive Listeria, and eukaryotic Toxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213's dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.
History
DepositionFeb 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)597,0484
Polymers596,4511
Non-polymers5973
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: 596451.250 Da / Num. of mol.: 1 / Mutation: N1045D
Source method: isolated from a genetically manipulated source
Details: N-terminally Strep-II tagged human RNF213, N1045D natural variant
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: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / 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: Human RNF213 / Type: COMPLEX
Details: E3 ubiquitin ligase RNF213, human, N1045D natural variant
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.59 MDa / Experimental 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
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen 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: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.86 sec. / Electron dose: 29.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143490 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00636080
ELECTRON MICROSCOPYf_angle_d0.47248785
ELECTRON MICROSCOPYf_dihedral_angle_d5.4684725
ELECTRON MICROSCOPYf_chiral_restr0.0375535
ELECTRON MICROSCOPYf_plane_restr0.0036189

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