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- EMDB-50922: Consensus refinement of the complex between human RNF213 and the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50922
TitleConsensus refinement of the complex between human RNF213 and the secreted effector IpaH2.5 from Shigella flexneri
Map dataConsensus refinement of the RNF213-IpaH2.5 complex (post-processed, auto-sharpened map)
Sample
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
KeywordsRNF213 / IpaH2.5 / IpaH / E3 ligase / RING / LRR / NEL / secreted effector / Shigella / inhibitor / complex / AAA / ATPase / ANTIMICROBIAL PROTEIN / CBM
Biological speciesHomo (humans)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: To Be Published
Title: Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213
Authors: Naydenova K / Boyle KB / Pathe C / Pothukuchi P / Crespillo-Casado A / Otten EG / Hammoudi P-M / Randow F
History
DepositionJul 7, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50922.png

Downloads & links

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Map

FileDownload / File: emd_50922.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus refinement of the RNF213-IpaH2.5 complex (post-processed, auto-sharpened map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 495. Å		1.24 Å/pix.
x 400 pix.
= 495. Å		1.24 Å/pix.
x 400 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07660065 - 0.17919365
Average (Standard dev.)0.00013220895 (±0.00237385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 494.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50922_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus refinement of the RNF213-IpaH2.5 complex (non-filtered, non-sharpened...

Fileemd_50922_additional_1.map
AnnotationConsensus refinement of the RNF213-IpaH2.5 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: Consensus refinement of the RNF213-IpaH2.5 complex (half map 1)

Fileemd_50922_half_map_1.map
AnnotationConsensus refinement of the RNF213-IpaH2.5 complex (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus refinement of the RNF213-IpaH2.5 complex (half map 2)

Fileemd_50922_half_map_2.map
AnnotationConsensus refinement of the RNF213-IpaH2.5 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 IpaH2.5 from Shi...

EntireName: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri
Components
  • Complex: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shigella flexneri

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Supramolecule #1: E3 ligase RNF213, bound to the secreted effector IpaH2.5 from Shi...

SupramoleculeName: E3 ligase RNF213, bound to the secreted effector IpaH2.5 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: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 23344 / Average exposure time: 1.75 sec. / Average electron dose: 40.0 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: 0.5 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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