+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36829 | |||||||||
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Title | Structure of Cas1-Cas2 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | IMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC | |||||||||
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: 3.6 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_36829.map.gz | 70.8 MB | EMDB map data format | |
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Header (meta data) | emd-36829-v30.xml emd-36829.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36829_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_36829.png | 57.3 KB | ||
Filedesc metadata | emd-36829.cif.gz | 5 KB | ||
Others | emd_36829_half_map_1.map.gz emd_36829_half_map_2.map.gz | 69.8 MB 69.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36829 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36829 | HTTPS FTP |
-Validation report
Summary document | emd_36829_validation.pdf.gz | 838.8 KB | Display | EMDB validaton report |
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Full document | emd_36829_full_validation.pdf.gz | 838.3 KB | Display | |
Data in XML | emd_36829_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | emd_36829_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36829 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36829 | HTTPS FTP |
-Related structure data
Related structure data | 8k26MC 8k21C 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_36829.map.gz / Format: CCP4 / Size: 75.1 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: 0.8374 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36829_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36829_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: Cas1
Macromolecule | Name: Cas1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 33.60348 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 NIKRLCMEN UniProtKB: Cas1 |
-Macromolecule #2: HD Cas3-type domain-containing protein
Macromolecule | Name: HD Cas3-type domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2004_A (virus) |
Molecular weight | Theoretical: 9.268722 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAMSDTGS VPKY UniProtKB: HD Cas3-type domain-containing protein |
-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 |