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Open data
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Basic information
Entry | Database: PDB / ID: 7oxa | ||||||
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Title | Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide | ||||||
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![]() | HYDROLASE / Cas9 / CRISPR / chRDNA / AAVS1 / nuclease | ||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Donohoue, P. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.T. / Gibson, J. ...Donohoue, P. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.T. / Gibson, J. / Kohrs, B. / Baek, K. / Owen, A.L.G. / Slorach, E.M. / van Overbeek, M. / Fuller, C.K. / May, A.P. / Jinek, M. / Cameron, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Authors: Donohoue, P.D. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.S. / Gibson, J. / Kohrs, B. / Baek, K. / Owen, A.L.G. / Slorach, E.M. / van ...Authors: Donohoue, P.D. / Pacesa, M. / Lau, E. / Vidal, B. / Irby, M.J. / Nyer, D.B. / Rotstein, T. / Banh, L. / Toh, M.S. / Gibson, J. / Kohrs, B. / Baek, K. / Owen, A.L.G. / Slorach, E.M. / van Overbeek, M. / Fuller, C.K. / May, A.P. / Jinek, M. / Cameron, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 739.2 KB | Display | ![]() |
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PDB format | ![]() | 568.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 332.7 KB | Display | ![]() |
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Full document | ![]() | 351.4 KB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ox7C ![]() 7ox8C ![]() 7ox9C ![]() 5fq5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 8446.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 3748.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-DNA/RNA hybrid / Protein , 2 types, 2 molecules AB
#1: DNA/RNA hybrid | Mass: 26124.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 158875.031 Da / Num. of mol.: 1 / Mutation: D10A, H840A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cas9, csn1, SPy_1046 / Plasmid: pMJ841 / Production host: ![]() ![]() References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
-Non-polymers , 3 types, 620 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/HOH.gif)
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#5: Chemical | #6: Chemical | ChemComp-K / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.66 Å / Num. obs: 113319 / % possible obs: 99.91 % / Redundancy: 6.8 % / Biso Wilson estimate: 46.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1128 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 11255 / CC1/2: 0.282 / % possible all: 99.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FQ5 Resolution: 2.15→47.66 Å / SU ML: 0.3167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7922 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: 70.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→47.66 Å
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Refine LS restraints |
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LS refinement shell |
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