+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41281 | |||||||||
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Title | CryoEM structure of Shedu 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: 2.9 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_41281.map.gz | 108.3 MB | EMDB map data format | |
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Header (meta data) | emd-41281-v30.xml emd-41281.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41281_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_41281.png | 113.2 KB | ||
Filedesc metadata | emd-41281.cif.gz | 5.8 KB | ||
Others | emd_41281_half_map_1.map.gz emd_41281_half_map_2.map.gz | 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41281 | HTTPS FTP |
-Validation report
Summary document | emd_41281_validation.pdf.gz | 897.8 KB | Display | EMDB validaton report |
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Full document | emd_41281_full_validation.pdf.gz | 897.3 KB | Display | |
Data in XML | emd_41281_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_41281_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41281 | HTTPS FTP |
-Related structure data
Related structure data | 8ti8MC 8ti9C 8tiaC M: atomic model generated by this map C: citing same article (ref.) |
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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_41281.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM structure of Shedu from Bacillus cereus | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_41281_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_41281_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 Tetramer
Entire | Name: Bacillus cereus Shedu Tetramer |
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Components |
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-Supramolecule #1: Bacillus cereus Shedu Tetramer
Supramolecule | Name: Bacillus cereus Shedu Tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus cereus B4264 (bacteria) |
Molecular weight | Theoretical: 175 KDa |
-Macromolecule #1: Shedu protein SduA
Macromolecule | Name: Shedu protein SduA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus cereus B4264 (bacteria) |
Molecular weight | Theoretical: 44.016969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNASDKINVW TTSRDSAVCG DIELKKTSTT RLIFRPEIVN NNKNPKASVR GCFIFQKKGR NALWDDYKEL DMNKLKAEEW IKLEINSDA MLTLTKEIQK HYAVHEKYGV RYGAFHLFKD NPDIEKLIEM FESNTDLLTQ LMEDDKSEAL EKTLEWIVTN D NPDKIIDR ...String: SNASDKINVW TTSRDSAVCG DIELKKTSTT RLIFRPEIVN NNKNPKASVR GCFIFQKKGR NALWDDYKEL DMNKLKAEEW IKLEINSDA MLTLTKEIQK HYAVHEKYGV RYGAFHLFKD NPDIEKLIEM FESNTDLLTQ LMEDDKSEAL EKTLEWIVTN D NPDKIIDR LKNLKEQDLD QLNTLIGIAN LKKVLSVWES NKLTNTSEKF WQSVLKENTW ILSQIFSNPT VLINDEAYVG GK TVKNDSG KLVDFLYANP FSKDAVLIEI KTPSTPLITP TEYRTGVYSA HKDLTGAVTQ VLTYKTTLQR EYQNIDYNNY RQG IKTDFD IITPCCVVIA GMFDTLTDTA HRHSFELYRK ELKNVTVITF DELFERVKGL IKLLEG 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 | 0.79 mg/mL | |||||||||||||||
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Buffer | pH: 8.5 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: GATAN K2 QUANTUM (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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8ti8: |