+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20182 | |||||||||
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Title | Dimeric DNA complex | |||||||||
Map data | dimeric DNA complex | |||||||||
Sample |
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Function / homology | CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain / Uncharacterized protein / Cpf1 Function and homology information | |||||||||
Biological species | Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.97 Å | |||||||||
Authors | Chang L / Li Z / Zhang H | |||||||||
Citation | Journal: Cell Host Microbe / Year: 2019 Title: Structural Basis for the Inhibition of CRISPR-Cas12a by Anti-CRISPR Proteins. Authors: Heng Zhang / Zhuang Li / Courtney M Daczkowski / Clinton Gabel / Andrew D Mesecar / Leifu Chang / Abstract: CRISPR-Cas12a (Cpf1), a type V CRISPR-associated nuclease, provides bacterial immunity against bacteriophages and plasmids but also serves as a tool for genome editing. Foreign nucleic acids are ...CRISPR-Cas12a (Cpf1), a type V CRISPR-associated nuclease, provides bacterial immunity against bacteriophages and plasmids but also serves as a tool for genome editing. Foreign nucleic acids are integrated into the CRISPR locus, prompting transcription of CRISPR RNAs (crRNAs) that guide Cas12a cleavage of foreign complementary DNA. However, mobile genetic elements counteract Cas12a with inhibitors, notably type V-A anti-CRISPRs (AcrVAs). We present cryoelectron microscopy structures of Cas12a-crRNA bound to AcrVA1 and AcrVA4 at 3.5 and 3.3 Å resolutions, respectively. AcrVA1 is sandwiched between the recognition (REC) and nuclease (NUC) lobes of Cas12a and inserts into the binding pocket for the protospacer-adjacent motif (PAM), a short DNA sequence guiding Cas12a targeting. AcrVA1 cleaves crRNA in a Cas12a-dependent manner, inactivating Cas12a-crRNA complexes. The AcrVA4 dimer is anchored around the crRNA pseudoknot of Cas12a-crRNA, preventing required conformational changes for crRNA-DNA heteroduplex formation. These results uncover molecular mechanisms for CRISPR-Cas12a inhibition, providing insights into bacteria-phage dynamics. | |||||||||
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_20182.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-20182-v30.xml emd-20182.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20182_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_20182.png | 61.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20182 | HTTPS FTP |
-Related structure data
Related structure data | 0445C 0446C 0447C 0449C 9398C 6nm9C 6nmaC 6nmcC 6nmdC 6nmeC 6omvC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20182.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | dimeric DNA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : dimeric DNA complex
Entire | Name: dimeric DNA complex |
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Components |
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-Supramolecule #1: dimeric DNA complex
Supramolecule | Name: dimeric DNA complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |