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Yorodumi- EMDB-29280: Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29280 | ||||||||||||||||||||||||||||||||||||
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Title | Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA | ||||||||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | DNA integration / maintenance of CRISPR repeat elements / IHF-DNA complex / Enzymes altering nucleic acid conformation / Site specific endodeoxyribonucleases: cleavage is not sequence specific / Nucleotidyltransferases / GO:0008301 / RECOMBINATION / DNA BINDING PROTEIN / HYDROLASE-DNA complex | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / DNA endonuclease activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / regulation of translation / chromosome / defense response to virus / DNA recombination / Hydrolases; Acting on ester bonds ...maintenance of CRISPR repeat elements / DNA endonuclease activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / regulation of translation / chromosome / defense response to virus / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) / synthetic construct (others) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||||||||||||||||||||||||||||||||
Authors | Santiago-Frangos A / Henriques WS / Wiegand T / Gauvin C / Buyukyoruk M / Neselu K / Eng ET / Lander GC / Wiedenheft B | ||||||||||||||||||||||||||||||||||||
Funding support | United States, 11 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Authors: Andrew Santiago-Frangos / William S Henriques / Tanner Wiegand / Colin C Gauvin / Murat Buyukyoruk / Ava B Graham / Royce A Wilkinson / Lenny Triem / Kasahun Neselu / Edward T Eng / Gabriel ...Authors: Andrew Santiago-Frangos / William S Henriques / Tanner Wiegand / Colin C Gauvin / Murat Buyukyoruk / Ava B Graham / Royce A Wilkinson / Lenny Triem / Kasahun Neselu / Edward T Eng / Gabriel C Lander / Blake Wiedenheft / Abstract: Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration ...Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560-kDa integration complex structure that explains how Pseudomonas aeruginosa Cas (Cas1-Cas2/3) and non-Cas proteins (for example, integration host factor) fold 150 base pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3 proteins rotate 100 degrees to expose DNA-binding sites on either side of the Cas2 homodimer, which each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5'-GT. Collectively, this work reveals new DNA-binding surfaces on Cas2 that are critical for DNA folding and site-specific delivery of foreign DNA. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29280.map.gz | 202.6 MB | EMDB map data format | |
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Header (meta data) | emd-29280-v30.xml emd-29280.xml | 32 KB 32 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29280_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_29280.png | 68 KB | ||
Filedesc metadata | emd-29280.cif.gz | 9 KB | ||
Others | emd_29280_half_map_1.map.gz emd_29280_half_map_2.map.gz | 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29280 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29280 | HTTPS FTP |
-Related structure data
Related structure data | 8fljMC 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_29280.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29280_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29280_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and ...
+Supramolecule #1: Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and ...
+Supramolecule #2: Cas1-Cas2/3 heterohexameric integrase
+Supramolecule #3: IHF heterodimer
+Supramolecule #4: CRISPR leader, repeat, and prespacer DNA annealed to mimic a half...
+Macromolecule #1: CRISPR-associated endonuclease Cas1
+Macromolecule #2: Integration host factor subunit alpha
+Macromolecule #3: Integration host factor subunit beta
+Macromolecule #8: CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
+Macromolecule #4: CRISPR leader, sense strand of DNA
+Macromolecule #5: CRISPR leader and repeat, anti-sense strand of DNA
+Macromolecule #6: CRISPR repeat and prespacer, sense strand of DNA
+Macromolecule #7: Prespacer, anti-sense strand of DNA
-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 R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. Details: Grids were glow discharged at 15 mA for 15 seconds with a 10 second hold (easiGlow, Pelco). | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 46860 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number real images: 10740 / Average exposure time: 2.5 sec. / Average electron dose: 69.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |