+Open data
-Basic information
Entry | Database: PDB / ID: 9cf0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Parasitella parasitica Fanzor (PpFz) State 1 | |||||||||
Components |
| |||||||||
Keywords | RNA BINDING PROTEIN/ISOMERASE/DNA / Fanzor / Eukaryotic / RNA-guided / nuclease / Gene editing / RNA BINDING PROTEIN-ISOMERASE-DNA complex | |||||||||
Function / homology | Function and homology information Set3 complex / negative regulation of meiotic nuclear division / ascospore formation / positive regulation of meiotic nuclear division / cyclosporin A binding / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport ...Set3 complex / negative regulation of meiotic nuclear division / ascospore formation / positive regulation of meiotic nuclear division / cyclosporin A binding / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to starvation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial intermembrane space / protein transport / protein folding / outer membrane-bounded periplasmic space / periplasmic space / mRNA binding / DNA damage response / mitochondrion / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) Parasitella parasitica (fungus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Xu, P. / Saito, M. / Zhang, F. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Cell / Year: 2024 Title: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Authors: Peiyu Xu / Makoto Saito / Guilhem Faure / Samantha Maguire / Samuel Chau-Duy-Tam Vo / Max E Wilkinson / Huihui Kuang / Bing Wang / William J Rice / Rhiannon K Macrae / Feng Zhang / Abstract: Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different ...Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different organisms. We find that Fzs share a common ωRNA interaction interface, regardless of the length of the ωRNA, which varies considerably across species. The analysis also reveals Fz's mode of DNA recognition and unwinding capabilities as well as the presence of a non-canonical catalytic site. The structures demonstrate how protein conformations of Fz shift to allow the binding of double-stranded DNA to the active site within the R-loop. Mechanistically, examination of structures in different states shows that the conformation of the lid loop on the RuvC domain is controlled by the formation of the guide/DNA heteroduplex, regulating the activation of nuclease and DNA double-stranded displacement at the single cleavage site. Our findings clarify the mechanism of Fz, establishing a foundation for engineering efforts. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9cf0.cif.gz | 453.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9cf0.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 9cf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cf0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9cf0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9cf0_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 9cf0_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/9cf0 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/9cf0 | HTTPS FTP |
-Related structure data
Related structure data | 45525MC 9cerC 9cesC 9cetC 9ceuC 9cevC 9cewC 9cexC 9ceyC 9cezC 9cf1C 9cf2C 9cf3C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 2 types, 2 molecules CP
#1: Protein | Mass: 17411.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CPR1, CPH1, CYP1, SCC1, YDR155C, YD8358.10C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14832, peptidylprolyl isomerase |
---|---|
#3: Protein | Mass: 144413.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parasitella parasitica (fungus) / Gene: malE, b4034, JW3994, PARPA_09356.1 scaffold 36248 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0AEX9, UniProt: A0A0B7NJM7 |
-DNA chain , 2 types, 2 molecules NT
#2: DNA chain | Mass: 17449.246 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: 17675.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-RNA chain / Non-polymers , 2 types, 2 molecules W
#5: RNA chain | Mass: 19514.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parasitella parasitica (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) |
---|---|
#6: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of PpFz1-omegaRNA-DNA / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Parasitella parasitica (fungus) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 48.47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15797 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.01 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|