+Open data
-Basic information
Entry | Database: PDB / ID: 7xf0 | ||||||
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Title | Crystal strucutre of CasDinG in complex with ATP | ||||||
Components | CasDinG | ||||||
Keywords | STRUCTURAL PROTEIN / Nuclease | ||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Zhang, J.T. / Cui, N. / Liu, Y.R. / Huang, H.D. / Jia, N. | ||||||
Funding support | 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment. Authors: Ning Cui / Jun-Tao Zhang / Yongrui Liu / Yanhong Liu / Xiao-Yu Liu / Chongyuan Wang / Hongda Huang / Ning Jia / Abstract: Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic ...Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying Csf complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the Csf complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xf0.cif.gz | 683.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xf0.ent.gz | 572.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xf0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7xf0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7xf0_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 7xf0_validation.cif.gz | 81.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/7xf0 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/7xf0 | HTTPS FTP |
-Related structure data
Related structure data | 7xexC 7xf1C 7xfzC 7xg0C 7xg2C 7xg3C 7xg4C 6fwrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 67939.883 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Sequence based on database WP_088922490.1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) #2: Chemical | Has ligand of interest | Y | |
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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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 6000, 0.1M HEPES 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 21, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→38.91 Å / Num. obs: 39721 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 67.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.069 / Rrim(I) all: 0.18 / Net I/σ(I): 9 / Num. measured all: 267256 / Scaling rejects: 1205 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FWR Resolution: 3.1→38.91 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.55 / Stereochemistry target values: ML
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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 max: 169.66 Å2 / Biso mean: 74.3619 Å2 / Biso min: 29.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→38.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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