+Open data
-Basic information
Entry | Database: PDB / ID: 8s9u | ||||||
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Title | CRISPR-Cas type III-D effector complex bound to a target RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / CRISPR / CRISPR-Cas / type III / complex / RNA / crRNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||
Authors | Schwartz, E.A. / Taylor, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Type III CRISPR-Cas effectors act as protein-assisted ribozymes Authors: Schwartz, E.A. / Bravo, J.P.K. / Ahsan, F. / Macias, L.A. / Brodbelt, J.S. / Brodbelt, J.S. / Palermo, G. / Fineran, P.C. / Fagerlund, R.D. / Taylor, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s9u.cif.gz | 524.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s9u.ent.gz | 407.9 KB | Display | PDB format |
PDBx/mmJSON format | 8s9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s9u_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8s9u_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8s9u_validation.xml.gz | 87.6 KB | Display | |
Data in CIF | 8s9u_validation.cif.gz | 134.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9u ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9u | HTTPS FTP |
-Related structure data
Related structure data | 40249MC 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
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 87558.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: sll7066 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZED2 |
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#2: Protein | Mass: 21899.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: sll7064 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZED4 |
#3: Protein | Mass: 64335.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: sll7067 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZED1 |
#4: Protein | Mass: 56820.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: sll7065 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZED3 |
#5: Protein | Mass: 90334.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: sll7063 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZED5 |
-RNA chain , 2 types, 2 molecules FG
#6: RNA chain | Mass: 11927.167 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Production host: Escherichia coli (E. coli) |
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#7: RNA chain | Mass: 19265.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synechocystis sp. PCC 6803 (bacteria) |
-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: CRISPR-Cas type III-D effector complex bound to target RNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: .351 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Particles were monodisperse and homogeneous. | |||||||||||||||||||||||||
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: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software | Name: cryoSPARC / Version: 3 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 609722 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.97 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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