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Yorodumi- PDB-8jg9: Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jg9 | |||||||||
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Title | Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer | |||||||||
Components |
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Keywords | VIRAL PROTEIN / II-A type anti-CRISPR protein | |||||||||
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 | Staphylococcus aureus (bacteria) Staphylococcus delphini (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å | |||||||||
Authors | Deng, X. / Wang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer Authors: Deng, X. / Wang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jg9.cif.gz | 548 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jg9.ent.gz | 438.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jg9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8jg9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jg9_validation.xml.gz | 77.6 KB | Display | |
Data in CIF | 8jg9_validation.cif.gz | 119.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/8jg9 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jg9 | HTTPS FTP |
-Related structure data
Related structure data | 36225MC 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
#1: Protein | Mass: 124158.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cas9 / Production host: Escherichia coli (E. coli) References: UniProt: J7RUA5, Hydrolases; Acting on ester bonds #2: RNA chain | Mass: 31304.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli DH5[alpha] (bacteria) #3: Protein | Mass: 20160.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus delphini (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) #4: DNA chain | | Mass: 7722.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus delphini (bacteria) #5: DNA chain | | Mass: 7627.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus delphini (bacteria) |
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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 | ||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72182 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |