+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36825 | |||||||||
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Title | ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (half form) | |||||||||
Map data | This is a composite map.The original map is mc2-half-overall.mrc | |||||||||
Sample |
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Keywords | IMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / endonuclease activity / hydrolase activity / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Vibrio phage ICP1_2004_A (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
Authors | Zhang LX / Feng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of csy complex with long DNA State2 Authors: Zhang LX / Feng Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36825.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-36825-v30.xml emd-36825.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36825_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_36825.png | 66.6 KB | ||
Filedesc metadata | emd-36825.cif.gz | 7.4 KB | ||
Others | emd_36825_additional_1.map.gz emd_36825_half_map_1.map.gz emd_36825_half_map_2.map.gz | 6.5 MB 98.5 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36825 | HTTPS FTP |
-Validation report
Summary document | emd_36825_validation.pdf.gz | 678.8 KB | Display | EMDB validaton report |
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Full document | emd_36825_full_validation.pdf.gz | 678.4 KB | Display | |
Data in XML | emd_36825_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_36825_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36825 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36825 | HTTPS FTP |
-Related structure data
Related structure data | 8k22MC 8k24C 8k29C 38838 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36825.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | This is a composite map.The original map is mc2-half-overall.mrc | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: This is a original map of mc2-single-overall-int-state.mrc
File | emd_36825_additional_1.map | ||||||||||||
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Annotation | This is a original map of mc2-single-overall-int-state.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36825_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36825_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : csy complex
+Supramolecule #1: csy complex
+Macromolecule #1: Csy1
+Macromolecule #2: Csy2
+Macromolecule #3: Cas1
+Macromolecule #4: Csy3
+Macromolecule #5: Csy4
+Macromolecule #9: HD Cas3-type domain-containing protein
+Macromolecule #6: RNA (60-MER)
+Macromolecule #7: DNA (43-MER)
+Macromolecule #8: DNA (31-MER)
+Macromolecule #10: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*...
+Macromolecule #11: MANGANESE (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |