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Yorodumi- EMDB-41282: CryoEM structure of octamer assembly of Shedu nuclease domain fro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41282 | |||||||||
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Title | CryoEM structure of octamer assembly of Shedu nuclease domain from Bacillus cereus | |||||||||
Map data | CryoEM structure of Shedu from Bacillus cereus | |||||||||
Sample |
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Keywords | Shedu / DUF4263 / Bacterial defense systems / Nuclease / Anti-plasmid defense system / PD-(D/E)XK nuclease / Whirly domain / Two-component signaling / DNA BINDING PROTEIN | |||||||||
Function / homology | Protein of unknown function DUF4263 / : / Shedu protein SduA, C-terminal / Shedu protein SduA, N-terminal / nuclease activity / defense response to virus / Shedu protein SduA Function and homology information | |||||||||
Biological species | Bacillus cereus B4264 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Gu Y / Corbett K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: to be published Title: Shedu anti-phage nucleases share a common enzymatic core regulated by diverse sensor domains Authors: Gu Y / Corbett K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41282.map.gz | 89.3 MB | EMDB map data format | |
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Header (meta data) | emd-41282-v30.xml emd-41282.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41282_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_41282.png | 94.1 KB | ||
Filedesc metadata | emd-41282.cif.gz | 6 KB | ||
Others | emd_41282_additional_1.map.gz emd_41282_additional_2.map.gz emd_41282_additional_3.map.gz emd_41282_half_map_1.map.gz emd_41282_half_map_2.map.gz | 89.6 MB 165.1 MB 165.1 MB 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41282 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41282 | HTTPS FTP |
-Related structure data
Related structure data | 8ti9MC 8tiaMC 8ti8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41282.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CryoEM structure of Shedu from Bacillus cereus | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.935 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: focused local refinement, main map
File | emd_41282_additional_1.map | ||||||||||||
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Annotation | focused local refinement, main map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused local refinement, half A map
File | emd_41282_additional_2.map | ||||||||||||
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Annotation | focused local refinement, half A map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused local refinement, half B map
File | emd_41282_additional_3.map | ||||||||||||
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Annotation | focused local refinement, half B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_41282_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_41282_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacillus cereus Shedu delta_NL octamer
Entire | Name: Bacillus cereus Shedu delta_NL octamer |
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Components |
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-Supramolecule #1: Bacillus cereus Shedu delta_NL octamer
Supramolecule | Name: Bacillus cereus Shedu delta_NL octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Octamer assembly of Bacillus cereus Shedu nuclease domain, which truncates the N-terminal and linker region. Glutamic acid 264 is mutated to Alanine. |
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Source (natural) | Organism: Bacillus cereus B4264 (bacteria) |
Molecular weight | Theoretical: 216 KDa |
-Macromolecule #1: Shedu protein SduA
Macromolecule | Name: Shedu protein SduA / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus cereus B4264 (bacteria) |
Molecular weight | Theoretical: 26.23676 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSSHHHHHH ENLYFQSNAK EQDLDQLNTL IGIANLKKVL SVWESNKLTN TSEKFWQSVL KENTWILSQI FSNPTVLIND EAYVGGKTV KNDSGKLVDF LYANPFSKDA VLIAIKTPST PLITPTEYRT GVYSAHKDLT GAVTQVLTYK TTLQREYQNI D YNNYRQGI ...String: MKSSHHHHHH ENLYFQSNAK EQDLDQLNTL IGIANLKKVL SVWESNKLTN TSEKFWQSVL KENTWILSQI FSNPTVLIND EAYVGGKTV KNDSGKLVDF LYANPFSKDA VLIAIKTPST PLITPTEYRT GVYSAHKDLT GAVTQVLTYK TTLQREYQNI D YNNYRQGI KTDFDIITPC CVVIAGMFDT LTDTAHRHSF ELYRKELKNV TVITFDELFE RVKGLIKLLE G UniProtKB: Shedu protein SduA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Prepared using deionized water and filtered strelized. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Freshly collected from size-exclusion column |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
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 | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-8ti9: PDB-8tia: |