+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31265 | |||||||||
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Title | Structure of Csy-AcrIF5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | complex / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA-DNA complex | |||||||||
Function / homology | Function and homology information CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) Similarity search - Domain/homology | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zhang L / Feng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Chem Biol / Year: 2022 Title: AcrIF5 specifically targets DNA-bound CRISPR-Cas surveillance complex for inhibition. Authors: Yongchao Xie / Laixing Zhang / Zhengyu Gao / Peipei Yin / Hao Wang / Hang Li / Zeliang Chen / Yi Zhang / Maojun Yang / Yue Feng / Abstract: CRISPR-Cas systems are prokaryotic antiviral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here we present structural and functional analyses of AcrIF5, exploring ...CRISPR-Cas systems are prokaryotic antiviral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here we present structural and functional analyses of AcrIF5, exploring its unique anti-CRISPR mechanism. AcrIF5 shows binding specificity only for the target DNA-bound form of the crRNA-guided surveillance (Csy) complex, but not the apo Csy complex from the type I-F CRISPR-Cas system. We solved the structure of the Csy-dsDNA-AcrIF5 complex, revealing that the conformational changes of the Csy complex caused by dsDNA binding dictate the binding specificity for the Csy-dsDNA complex by AcrIF5. Mechanistically, five AcrIF5 molecules bind one Csy-dsDNA complex, which destabilizes the helical bundle domain of Cas8f, thus preventing subsequent Cas2/3 recruitment. AcrIF5 exists in symbiosis with AcrIF3, which blocks Cas2/3 recruitment. This attack on the recruitment event stands in contrast to the conventional mechanisms of blocking binding of target DNA. Overall, our study reveals an unprecedented mechanism of CRISPR-Cas inhibition by AcrIF5. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31265.map.gz | 6.2 MB | EMDB map data format | |
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Header (meta data) | emd-31265-v30.xml emd-31265.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31265_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_31265.png | 55 KB | ||
Filedesc metadata | emd-31265.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31265 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31265 | HTTPS FTP |
-Validation report
Summary document | emd_31265_validation.pdf.gz | 439.7 KB | Display | EMDB validaton report |
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Full document | emd_31265_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | emd_31265_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_31265_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31265 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31265 | HTTPS FTP |
-Related structure data
Related structure data | 7eqgMC 7f45C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31265.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:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Csy-AcrIF5
+Supramolecule #1: Csy-AcrIF5
+Supramolecule #2: Csy-AcrIF5
+Supramolecule #3: DNA
+Macromolecule #1: CRISPR type I-F/YPEST-associated protein Csy2
+Macromolecule #2: CRISPR-associated protein Csy3
+Macromolecule #3: AcrIF5
+Macromolecule #4: type I-F CRISPR-associated endoribonuclease Cas6/Csy4
+Macromolecule #7: Type I-F CRISPR-associated protein Csy1
+Macromolecule #5: RNA (60-MER)
+Macromolecule #6: DNA (54-MER)
+Macromolecule #8: DNA (54-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |