+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19658 | |||||||||
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Title | Human RNF213: focused refinement of E3 ligase domain | |||||||||
Map data | Unsharpened map of RNF213 E3 ligase domain after focused refinement | |||||||||
Sample |
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Keywords | E3 ubiquitin ligase / ANTIMICROBIAL PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Naydenova K / Randow F | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Embo J. / 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 #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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19658.map.gz | 475 MB | EMDB map data format | |
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Header (meta data) | emd-19658-v30.xml emd-19658.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19658_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_19658.png | 59.3 KB | ||
Masks | emd_19658_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-19658.cif.gz | 4.7 KB | ||
Others | emd_19658_half_map_1.map.gz emd_19658_half_map_2.map.gz | 413.4 MB 413.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19658 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19658 | HTTPS FTP |
-Validation report
Summary document | emd_19658_validation.pdf.gz | 947.3 KB | Display | EMDB validaton report |
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Full document | emd_19658_full_validation.pdf.gz | 946.9 KB | Display | |
Data in XML | emd_19658_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | emd_19658_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19658 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19658 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19658.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened map of RNF213 E3 ligase domain after focused refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.921 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19658_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map (2) of RNF213 E3 ligase domain focused refinement
File | emd_19658_half_map_1.map | ||||||||||||
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Annotation | Half-map (2) of RNF213 E3 ligase domain focused refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map (1) of RNF213 E3 ligase domain focused refinement
File | emd_19658_half_map_2.map | ||||||||||||
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Annotation | Half-map (1) of RNF213 E3 ligase domain focused refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human RNF213
Entire | Name: Human RNF213 |
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Components |
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-Supramolecule #1: Human RNF213
Supramolecule | Name: Human RNF213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: E3 ubiquitin ligase RNF213, human, N1045D natural variant |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 590 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: AB INITIO MODEL |