+Open data
-Basic information
Entry | Database: PDB / ID: 8hr5 | ||||||||||||
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Title | Cryo-EM structure of the CnCas12f1-sgRNA-DNA complex | ||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA/DNA / Complex / CRISPR-Cas / RNA BINDING PROTEIN-RNA-DNA complex | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Clostridium novyi (bacteria) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.73 Å | ||||||||||||
Authors | Li, F. / Ji, Q. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Structure and engineering of miniature Clostridium novyi CRISPR-Cas12f1 with rare C-rich PAM specificity Authors: Li, F. / Ji, Q. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hr5.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hr5.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/8hr5 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/8hr5 | HTTPS FTP |
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-Related structure data
Related structure data | 34958MC 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: 58609.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium novyi (bacteria) / Gene: DFH04_07400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A386YN77 #2: RNA chain | | Mass: 75498.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: DNA chain | | Mass: 8612.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #4: DNA chain | | Mass: 5547.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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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: Ternary complex of CnCas12f1-sgRNA-DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Clostridium novyi (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-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 FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100719 / Symmetry type: POINT | ||||||||||||||||||||||||
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