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Yorodumi- PDB-8pj9: Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pj9 | ||||||
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Title | Cas9 bound to cognate DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Cas9 / CRISPR-Cas / PAM / spacer acquisition | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus thermophilus DGCC 7710 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å | ||||||
Authors | Sasnauskas, G. / Gaizauskaite, U. / Tamulaitiene, G. | ||||||
Funding support | Lithuania, 1items
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Citation | Journal: To Be Published Title: Structural basis for spacer acquisition in a type II-A CRISPR-Cas system Authors: Sasnauskas, G. / Gaizauskaite, U. / Tamulaitiene, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pj9.cif.gz | 333.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pj9.ent.gz | 228.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pj9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8pj9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8pj9_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 8pj9_validation.cif.gz | 67.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/8pj9 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/8pj9 | HTTPS FTP |
-Related structure data
Related structure data | 17702MC 8pk1C 8pig M: map data used to model this data 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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1 |
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-Components
-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 13609.083 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Streptococcus thermophilus DGCC 7710 (bacteria) |
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#3: RNA chain | Mass: 24119.357 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Streptococcus thermophilus DGCC 7710 (bacteria) References: GenBank: 343794779 |
-DNA oligoduplex, ... , 2 types, 3 molecules DEF
#4: DNA chain | Mass: 9670.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: DNA chain | | Mass: 3718.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Protein / Non-polymers , 2 types, 2 molecules A
#1: Protein | Mass: 162498.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus DGCC 7710 (bacteria) Gene: cas9, csn1 Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) References: UniProt: G3ECR1, Hydrolases; Acting on ester bonds |
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#6: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 46.33 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1744 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 894269 / Details: Blob picking in cryoSPARC live session | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119790 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE |