9UDI | pdb_00009udi

Cryo-EM structure of the RdCas12n-sgRNA-DNA ternary complex, Conformation 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanisms and engineering of a miniature type V-N CRISPR-Cas12 effector enzyme.

Fu, W.Ma, J.Wang, Z.Tang, N.Pan, D.Su, M.Wu, Z.Gan, J.Ji, Q.

(2025) Nat Commun 16: 5667-5667

  • DOI: https://doi.org/10.1038/s41467-025-61290-3
  • Primary Citation of Related Structures:  
    9J09, 9UDI

  • PubMed Abstract: 

    Type V CRISPR-Cas12 systems are highly diverse in their functionality and molecular compositions, including miniature Cas12f1 and Cas12n genome editors that provide advantages for efficient in vivo therapeutic delivery due to their small size. In contrast to Cas12f1 nucleases that utilize a homodimer structure for DNA targeting and cleavage with a preference for T- or C-rich PAMs, Cas12n nucleases are likely monomeric proteins and uniquely recognize rare A-rich PAMs. However, the molecular mechanisms behind RNA-guided genome targeting and cleavage by Cas12n remain unclear. Here, we present the cryo-electron microscopy (cryo-EM) structure of Rothia dentocariosa Cas12n (RdCas12n) bound to a single guide RNA (sgRNA) and target DNA, illuminating the intricate molecular architecture of Cas12n and its sgRNA, as well as PAM recognition and nucleic-acid binding mechanisms. Through structural comparisons with other Cas12 nucleases and the ancestral precursor TnpB, we provide insights into the evolutionary significance of Cas12n in the progression from TnpB to various Cas12 nucleases. Additionally, we extensively modify the sgRNA and convert RdCas12n into an effective genome editor in human cells. Our findings enhance the understanding of the evolutionary mechanisms of type V CRISPR-Cas12 systems and offer a molecular foundation for engineering Cas12n genome editors.


  • Organizational Affiliation
    • School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transposase540Rothia dentocariosaMutation(s): 0 
Gene Names: HXO56_11955
UniProt
Find proteins for A0A7D4LAR1 (Rothia dentocariosa)
Explore A0A7D4LAR1 
Go to UniProtKB:  A0A7D4LAR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7D4LAR1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (40-MER)B [auth C]40synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*TP*GP*TP*GP*AP*GP*AP*AP*AP*CP*CP*G)-3')C [auth D]14synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
sgRNAD [auth R]214Rothia dentocariosa
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-06-04 
  • Deposition Author(s): Fu, W., Ji, Q.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21922705
National Natural Science Foundation of China (NSFC)China2207783
National Natural Science Foundation of China (NSFC)China91753127

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references