+Open data
-Basic information
Entry | Database: PDB / ID: 6xmg | ||||||
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Title | Cryo-EM structure of Cas12g ternary complex | ||||||
Components |
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Keywords | HYDROLASE/RNA / CRISPR / HYDROLASE-RNA complex | ||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Chang, L. / Li, Z. / Zhang, H. | ||||||
Citation | Journal: Nat Chem Biol / Year: 2021 Title: Cryo-EM structure of the RNA-guided ribonuclease Cas12g. Authors: Zhuang Li / Heng Zhang / Renjian Xiao / Ruijie Han / Leifu Chang / Abstract: Cas12g, the type V-G CRISPR-Cas effector, is an RNA-guided ribonuclease that targets single-stranded RNA substrate. The CRISPR-Cas12g system offers a potential platform for transcriptome engineering ...Cas12g, the type V-G CRISPR-Cas effector, is an RNA-guided ribonuclease that targets single-stranded RNA substrate. The CRISPR-Cas12g system offers a potential platform for transcriptome engineering and diagnostic applications. We determined the structures of Cas12g-guide RNA complexes in the absence and presence of target RNA by cryo-EM to a resolution of 3.1 Å and 4.8 Å, respectively. Cas12g adopts a bilobed structure with miniature REC2 and Nuc domains, whereas the guide RNAs fold into a flipped 'F' shape, which is primarily recognized by the REC lobe. Target RNA and the CRISPR RNA (crRNA) guide form a duplex that inserts into the central cavity between the REC and NUC lobes, inducing conformational changes in both lobes to activate Cas12g. The structural insights would facilitate the development of Cas12g-based applications. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xmg.cif.gz | 203.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xmg.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xmg_validation.pdf.gz | 743.3 KB | Display | wwPDB validaton report |
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Full document | 6xmg_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | 6xmg_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 6xmg_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xmg ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xmg | HTTPS FTP |
-Related structure data
Related structure data | 22258MC 6xmfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 89891.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: hot spring metagenome / Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: RNA chain | Mass: 43777.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: hot spring metagenome / Source: (synth.) metagenome (others) |
#3: RNA chain | Mass: 7633.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: hot spring metagenome / Source: (synth.) metagenome (others) |
#4: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-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: CRISP-Cas complex / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: metagenome (others) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38238 / Symmetry type: POINT | ||||||||||||||||||||||||
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