9CF3

Parasitella parasitica Fanzor (PpFz) State 4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights into the diversity and DNA cleavage mechanism of Fanzor.

Xu, P.Saito, M.Faure, G.Maguire, S.Chau-Duy-Tam Vo, S.Wilkinson, M.E.Kuang, H.Wang, B.Rice, W.J.Macrae, R.K.Zhang, F.

(2024) Cell 187: 5238-5252.e20

  • DOI: https://doi.org/10.1016/j.cell.2024.07.050
  • Primary Citation of Related Structures:  
    9CER, 9CES, 9CET, 9CEU, 9CEV, 9CEW, 9CEX, 9CEY, 9CEZ, 9CF0, 9CF1, 9CF2, 9CF3

  • PubMed 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 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.


  • Organizational Affiliation

    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseB [auth C]162Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CPR1CPH1CYP1SCC1YDR155CYD8358.10C
EC: 5.2.1.8
UniProt
Find proteins for P14832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14832 
Go to UniProtKB:  P14832
Entity Groups  
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UniProt GroupP14832
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1D [auth P]1,259Parasitella parasiticaMutation(s): 0 
Gene Names: malEb4034JW3994PARPA_09356.1 scaffold 36248
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for A0A0B7NJM7 (Parasitella parasitica)
Explore A0A0B7NJM7 
Go to UniProtKB:  A0A0B7NJM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0B7NJM7P0AEX9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
Parasitella parasitica Fanzor 1 omegaRNAA [auth W]61Parasitella parasitica
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA non-target strandC [auth N]57synthetic construct
Sequence Annotations
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA target strandE [auth T]57synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 2.0: 2024-09-25
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-02
    Changes: Data collection, Database references