+Open data
-Basic information
Entry | Database: PDB / ID: 8pm4 | ||||||
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Title | Cryo-EM structure of the Cas12m-crRNA-target DNA complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Cas12 / Cas12m / CRISPR-Cas / RuvC / crRNA / PAM | ||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) / Transposase Function and homology information | ||||||
Biological species | Gordonia otitidis NBRC 100426 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
Authors | Sasnauskas, G. / Tamulaitiene, G. / Karvelis, T. / Bigelyte, G. / Siksnys, V. | ||||||
Funding support | Lithuania, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing. Authors: Greta Bigelyte / Brigita Duchovska / Rimante Zedaveinyte / Giedrius Sasnauskas / Tomas Sinkunas / Indre Dalgediene / Giedre Tamulaitiene / Arunas Silanskas / Darius Kazlauskas / Lukas ...Authors: Greta Bigelyte / Brigita Duchovska / Rimante Zedaveinyte / Giedrius Sasnauskas / Tomas Sinkunas / Indre Dalgediene / Giedre Tamulaitiene / Arunas Silanskas / Darius Kazlauskas / Lukas Valančauskas / Julene Madariaga-Marcos / Ralf Seidel / Virginijus Siksnys / Tautvydas Karvelis / Abstract: Cas9 and Cas12 nucleases of class 2 CRISPR-Cas systems provide immunity in prokaryotes through RNA-guided cleavage of foreign DNA. Here we characterize a set of compact CRISPR-Cas12m (subtype V-M) ...Cas9 and Cas12 nucleases of class 2 CRISPR-Cas systems provide immunity in prokaryotes through RNA-guided cleavage of foreign DNA. Here we characterize a set of compact CRISPR-Cas12m (subtype V-M) effector proteins and show that they provide protection against bacteriophages and plasmids through the targeted DNA binding rather than DNA cleavage. Biochemical assays suggest that Cas12m effectors can act as roadblocks inhibiting DNA transcription and/or replication, thereby triggering interference against invaders. Cryo-EM structure of Gordonia otitidis (Go) Cas12m ternary complex provided here reveals the structural mechanism of DNA binding ensuring interference. Harnessing GoCas12m innate ability to bind DNA target we fused it with adenine deaminase TadA-8e and showed an efficient A-to-G editing in Escherichia coli and human cells. Overall, this study expands our understanding of the functionally diverse Cas12 protein family, revealing DNA-binding dependent interference mechanism of Cas12m effectors that could be harnessed for engineering of compact base-editing tools. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pm4.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pm4.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 8pm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pm4 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pm4 | HTTPS FTP |
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-Related structure data
Related structure data | 17757MC 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: 68223.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cas12m protein Source: (gene. exp.) Gordonia otitidis NBRC 100426 (bacteria) Gene: GOOTI_202_00040 Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) References: UniProt: H5TRP0 |
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#2: RNA chain | Mass: 18751.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gordonia otitidis NBRC 100426 (bacteria) |
#3: DNA chain | Mass: 13556.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 13543.744 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: Cas12m protein in complex with crRNA and cognate DNA, Gordonia otitidis NBRC 100426 system Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Gordonia otitidis NBRC 100426 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli str. K-12 substr. DH10B (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 46.33 sec. / Electron dose: 29.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2032 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204822 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.78 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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