+Open data
-Basic information
Entry | Database: PDB / ID: 8hns | ||||||
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Title | Crystal structure of an anti-CRISPR protein AcrIIC4 in apo form | ||||||
Components | anti-CRISPR protein AcrIIC4 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / anti-CRISPR protein / cleavage inhibition / dimer | ||||||
Biological species | Haemophilus parainfluenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Sun, W. / Cheng, Z. / Yang, J. / Wang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation. Authors: Wei Sun / Zhi Cheng / Jiuyu Wang / Jing Yang / Xueyan Li / Jinlong Wang / Minxuan Chen / Xiaoqi Yang / Gang Sheng / Jizhong Lou / Yanli Wang / Abstract: Anti-CRISPR (Acr) proteins are encoded by phages and other mobile genetic elements and inhibit host CRISPR-Cas immunity using versatile strategies. AcrIIC4 is a broad-spectrum Acr that inhibits the ...Anti-CRISPR (Acr) proteins are encoded by phages and other mobile genetic elements and inhibit host CRISPR-Cas immunity using versatile strategies. AcrIIC4 is a broad-spectrum Acr that inhibits the type II-C CRISPR-Cas9 system in several species by an unknown mechanism. Here, we determined a series of structures of Cas9 (HpaCas9)-sgRNA in complex with AcrIIC4 and/or target DNA, as well as the crystal structure of AcrIIC4 alone. We found that AcrIIC4 resides in the crevice between the REC1 and REC2 domains of HpaCas9, where its extensive interactions restrict the mobility of the REC2 domain and prevent the unwinding of target double-stranded (ds) DNA at the PAM-distal end. Therefore, the full-length guide RNA:target DNA heteroduplex fails to form in the presence of AcrIIC4, preventing Cas9 nuclease activation. Altogether, our structural and biochemical studies illuminate a unique Acr mechanism that allows DNA binding to the Cas9 effector complex but blocks its cleavage by preventing R-loop formation, a key step supporting DNA cleavage by Cas9. #1: Journal: mBio / Year: 2018 Title: Potent Cas9 Inhibition in Bacterial and Human Cells by AcrIIC4 and AcrIIC5 Anti-CRISPR Proteins. Authors: Lee, J. / Mir, A. / Edraki, A. / Garcia, B. / Amrani, N. / Lou, H.E. / Gainetdinov, I. / Pawluk, A. / Ibraheim, R. / Gao, X.D. / Liu, P. / Davidson, A.R. / Maxwell, K.L. / Sontheimer, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hns.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hns.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/8hns ftp://data.pdbj.org/pub/pdb/validation_reports/hn/8hns | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10072.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: WP_049372635.1;The first residue 'Ser' of the sample sequence is the one expressed from the vector left after tag cleavage. Source: (gene. exp.) Haemophilus parainfluenzae (bacteria) / Gene: acrIIC4 / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: tris, sodium chloride, sodium acetate, PEG 3350, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→50 Å / Num. obs: 6556 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 2.54→2.58 Å / Rmerge(I) obs: 0.83 / Num. unique obs: 328 / CC1/2: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model ( the crystal structure of a SeMet-derivative of this protein using SAD) Resolution: 2.54→37.2 Å / SU ML: 0.2404 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.6182 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→37.2 Å
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Refine LS restraints |
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LS refinement shell |
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