+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36824 | |||||||||
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Title | Cas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | IMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC/RNA BINDING PROTEIN/DNA / ANTIBIOTIC-RNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / 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: 3.8 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 short DNA 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_36824.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-36824-v30.xml emd-36824.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36824_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_36824.png | 34.6 KB | ||
Filedesc metadata | emd-36824.cif.gz | 5.5 KB | ||
Others | emd_36824_half_map_1.map.gz emd_36824_half_map_2.map.gz | 40.8 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36824 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36824 | HTTPS FTP |
-Validation report
Summary document | emd_36824_validation.pdf.gz | 796 KB | Display | EMDB validaton report |
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Full document | emd_36824_full_validation.pdf.gz | 795.6 KB | Display | |
Data in XML | emd_36824_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_36824_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36824 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36824 | HTTPS FTP |
-Related structure data
Related structure data | 8k21MC 8k26C 8k27C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36824.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Half map: #2
File | emd_36824_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36824_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : csy complex
Entire | Name: csy complex |
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Components |
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-Supramolecule #1: csy complex
Supramolecule | Name: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
-Macromolecule #1: DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP...
Macromolecule | Name: DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3') type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 6.543286 KDa |
Sequence | String: (DA)(DG)(DC)(DA)(DA)(DT)(DT)(DT)(DA)(DA) (DA)(DT)(DA)(DG)(DG)(DG)(DA)(DA)(DG)(DA) (DT) |
-Macromolecule #2: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*...
Macromolecule | Name: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3') type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 6.33812 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DT)(DC)(DC)(DC)(DT)(DA) (DT)(DT)(DT)(DA)(DA)(DA)(DT)(DT)(DG)(DC) (DT) |
-Macromolecule #3: HD Cas3-type domain-containing protein
Macromolecule | Name: HD Cas3-type domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 8.332723 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAM UniProtKB: HD Cas3-type domain-containing protein |
-Macromolecule #4: Cas1
Macromolecule | Name: Cas1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 33.489379 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH ...String: MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH EGTFVKSLYK EYALEYEIEF KRDHKSADNY NKFLTLGNYY AYGIARSSLW ALGIDNSFPL LHGSTRRGGL VF DVADIIK TSIILPLAFH AADQGMSNTE FKRSCVAYFD KNDILAYLIN NIKRLCME UniProtKB: Cas1 |
-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 |