+Open data
-Basic information
Entry | Database: PDB / ID: 8hud | |||||||||
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Title | Cryo-EM structure of the EvCas9-sgRNA-target DNA ternary complex | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / RNA / DNA / RNA BINDING PROTEIN-RNA-DNA complex | |||||||||
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 | Eubacterium ventriosum ATCC 27560 (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
Authors | Tang, N. / Wu, Z. / Gao, Y. / Chen, W. / Su, M. / Wang, Z. / Ji, Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the EvCas9-sgRNA-target DNA ternary complex Authors: Tang, N. / Wu, Z. / Gao, Y. / Chen, W. / Wang, Z. / Su, M. / Ji, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hud.cif.gz | 224.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hud.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 8hud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hud_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8hud_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8hud_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 8hud_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/8hud ftp://data.pdbj.org/pub/pdb/validation_reports/hu/8hud | HTTPS FTP |
-Related structure data
Related structure data | 35035MC 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: 131110.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium ventriosum ATCC 27560 (bacteria) Gene: csn1, cas9, EUBVEN_00141 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A5Z395, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 23976.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 8641.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2467.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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: Ternary complex of EvCas9-sgRNA-dsDNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.1565 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Eubacterium ventriosum ATCC 27560 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28a | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Homemade | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 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 defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 16.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Num. of particles selected: 300599 | ||||||||||||
3D reconstruction | Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33599 / Symmetry type: POINT |