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- EMDB-19656: Human RNF213: focused refinement of stalk domain -

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Basic information

Entry
Database: EMDB / ID: EMD-19656
TitleHuman RNF213: focused refinement of stalk domain
Map dataUnsharpened map of RNF213 stalk domain after focused refinement
Sample
  • Complex: Human RNF213
KeywordsE3 ubiquitin ligase / ANTIMICROBIAL PROTEIN
Biological speciesHomo sapiens (human)
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
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2024
Title: Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213
Authors: Casado AC / Pothukuchi P / Naydenova K / Yip MCJ / Young JM / Boulanger J / Dharamdasani V / Harper C / Hammoudi PM / Otten EG / Boyle K / Gogoi M / Malik HS / Randow F
History
DepositionFeb 16, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19656.png

Downloads & links

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Map

FileDownload / File: emd_19656.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of RNF213 stalk domain after focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.552 Å		0.92 Å/pix.
x 512 pix.
= 471.552 Å		0.92 Å/pix.
x 512 pix.
= 471.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02129041 - 0.05472094
Average (Standard dev.)-0.000012422966 (±0.00063248293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19656_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map (1) of RNF213 stalk domain focused refinement

Fileemd_19656_half_map_1.map
AnnotationHalf-map (1) of RNF213 stalk domain focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map (2) of RNF213 stalk domain focused refinement

Fileemd_19656_half_map_2.map
AnnotationHalf-map (2) of RNF213 stalk domain focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human RNF213

EntireName: Human RNF213
Components
  • Complex: Human RNF213

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Supramolecule #1: Human RNF213

SupramoleculeName: Human RNF213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: E3 ubiquitin ligase RNF213, human, N1045D natural variant
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 590 KDa

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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 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 4.86 sec. / Average electron dose: 29.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 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: 143490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL

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