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Yorodumi- EMDB-17722: Cas1-Cas2 CRISPR integrase bound to prespacer DNA, Streptococcus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17722 | |||||||||
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Title | Cas1-Cas2 CRISPR integrase bound to prespacer DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system | |||||||||
Map data | Map autosharpened using phenix.auto_sharpen_1.21rc1-4903 b_iso_to_d_cut and 3.17 A cutoff | |||||||||
Sample |
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Keywords | Cas1-Cas2 integrase / CRISPR-Cas / prespacer / spacer acquisition / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Streptococcus thermophilus DGCC 7710 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Sasnauskas G / Gaizauskaite U / Tamulaitiene G | |||||||||
Funding support | Lithuania, 1 items
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Citation | Journal: To Be Published Title: Structural basis for spacer acquisition in a type II-A CRISPR-Cas system Authors: Sasnauskas G / Gaizauskaite U / Tamulaitiene G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17722.map.gz | 112.3 MB | EMDB map data format | |
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Header (meta data) | emd-17722-v30.xml emd-17722.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17722_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_17722.png | 147.4 KB | ||
Masks | emd_17722_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-17722.cif.gz | 6.5 KB | ||
Others | emd_17722_additional_1.map.gz emd_17722_half_map_1.map.gz emd_17722_half_map_2.map.gz | 62.8 MB 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17722 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17722 | HTTPS FTP |
-Validation report
Summary document | emd_17722_validation.pdf.gz | 885.7 KB | Display | EMDB validaton report |
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Full document | emd_17722_full_validation.pdf.gz | 885.3 KB | Display | |
Data in XML | emd_17722_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_17722_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17722 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17722 | HTTPS FTP |
-Related structure data
Related structure data | 8pk1MC 8pj9C 8q2nC 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_17722.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map autosharpened using phenix.auto_sharpen_1.21rc1-4903 b_iso_to_d_cut and 3.17 A cutoff | ||||||||||||||||||||
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
-Mask #1
File | emd_17722_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_17722_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17722_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17722_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cas1-Cas2 CRISPR integrase-prespacer DNA complex
Entire | Name: Cas1-Cas2 CRISPR integrase-prespacer DNA complex |
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Components |
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-Supramolecule #1: Cas1-Cas2 CRISPR integrase-prespacer DNA complex
Supramolecule | Name: Cas1-Cas2 CRISPR integrase-prespacer DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Streptococcus thermophilus DGCC 7710 (bacteria) |
-Macromolecule #1: CRISPR-associated endoribonuclease Cas2
Macromolecule | Name: CRISPR-associated endoribonuclease Cas2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Streptococcus thermophilus DGCC 7710 (bacteria) |
Molecular weight | Theoretical: 13.43156 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSYRYMRMIL MFDMPTDTAE ERKAYRKFRK FLLSEGFIMH QFSVYSKLLL NHTANTAMVG RLKANNPKKG NITILTVTEK QFARMIYLY GDKNTSIANS EERLVFLGDN YCDED UniProtKB: CRISPR-associated endoribonuclease Cas2 |
-Macromolecule #2: CRISPR-associated endonuclease Cas1
Macromolecule | Name: CRISPR-associated endonuclease Cas1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Streptococcus thermophilus DGCC 7710 (bacteria) |
Molecular weight | Theoretical: 35.363461 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAGWRTVVVN IHSKLSYKNN HLIFRNSYKT EMIHLSEIDI LLLETTDIVL TTMLVKRLVD ENILVIFCDD KRLPTAFLTP YYARHDSSL QIARQIAWKE NVKCEVWTAI IAQKILNQSY YLGECSFFEK SQSIMELYHG LERFDPSNRE GHSARIYFNT L FGNDFTRE ...String: MAGWRTVVVN IHSKLSYKNN HLIFRNSYKT EMIHLSEIDI LLLETTDIVL TTMLVKRLVD ENILVIFCDD KRLPTAFLTP YYARHDSSL QIARQIAWKE NVKCEVWTAI IAQKILNQSY YLGECSFFEK SQSIMELYHG LERFDPSNRE GHSARIYFNT L FGNDFTRE SDNDINAALD YGYTLLLSMF AREVVVCGCM TQIGLKHANQ FNQFNLASDI MEPFRPIIDR IVYQNRHNNF VK IKKELFS IFSETYLYNG KEMYLSNIVS DYTKKVIKAL NQLGEEIPEF RILESGWSHP QFEKA UniProtKB: CRISPR-associated endonuclease Cas1 |
-Macromolecule #3: Chains: G,J
Macromolecule | Name: Chains: G,J / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.917082 KDa |
Sequence | String: (DT)(DT)(DT)(DA)(DC)(DT)(DA)(DC)(DT)(DC) (DG)(DT)(DT)(DC)(DT)(DG)(DG)(DT)(DG)(DT) (DT)(DT)(DC)(DT)(DC)(DG) |
-Macromolecule #4: Chains: H,K
Macromolecule | Name: Chains: H,K / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 8.062258 KDa |
Sequence | String: (DA)(DA)(DA)(DC)(DA)(DC)(DC)(DA)(DG)(DA) (DA)(DC)(DG)(DA)(DG)(DT)(DA)(DG)(DT)(DA) (DA)(DA)(DT)(DT)(DG)(DG) |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 3373 / Average exposure time: 46.33 sec. / Average electron dose: 30.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000 |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8pk1: |