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Yorodumi- PDB-8pk1: Cas1-Cas2 CRISPR integrase bound to prespacer DNA, Streptococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pk1 | ||||||
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Title | Cas1-Cas2 CRISPR integrase bound to prespacer DNA, Streptococcus thermophilus DGCC 7710 CRISPR3 system | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Cas1-Cas2 integrase / CRISPR-Cas / prespacer / spacer acquisition | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA 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: 3.17 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 | 8pk1.cif.gz | 329 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pk1.ent.gz | 233.9 KB | Display | PDB format |
PDBx/mmJSON format | 8pk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pk1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8pk1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8pk1_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 8pk1_validation.cif.gz | 83.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/8pk1 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pk1 | HTTPS FTP |
-Related structure data
Related structure data | 17722MC 8pj9C 8pig 8pmh C: citing same article (ref.) M: map data used to model this data |
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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
#1: Protein | Mass: 13431.560 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus DGCC 7710 (bacteria) Gene: cas2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3ECR3, Hydrolases; Acting on ester bonds #2: Protein | Mass: 35363.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus DGCC 7710 (bacteria) Gene: cas1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3ECR2, Hydrolases; Acting on ester bonds #3: DNA chain | Mass: 7917.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 8062.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Chemical | 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 | Name: Cas1-Cas2 CRISPR integrase-prespacer DNA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: Streptococcus thermophilus DGCC 7710 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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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: 30.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 3373 |
-Processing
EM software | Name: PHENIX / Version: 1.21rc1_4903 / Category: model refinement |
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CTF correction | Type: NONE |
Particle selection | Details: Blob picking in cryoSPARC live session |
3D reconstruction | Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91658 / Symmetry type: POINT |
Atomic model building | Source name: AlphaFold / Type: in silico model |
Refinement | Cross valid method: NONE |