7YOJ

Structure of CasPi with guide RNA and target DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Resolution: 3.36 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

The compact Cas pi (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation.

Sun, A.Li, C.P.Chen, Z.Zhang, S.Li, D.Y.Yang, Y.Li, L.Q.Zhao, Y.Wang, K.Li, Z.Liu, J.Liu, S.Wang, J.Liu, J.G.

(2023) Cell Res 33: 229-244

  • DOI: https://doi.org/10.1038/s41422-022-00771-2
  • Primary Citation of Related Structures:  
    7YOJ

  • PubMed Abstract: 

    CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CasPi867Armatimonadota bacteriumMutation(s): 2 
Gene Names: DCC45_12200EDM73_08925
UniProt
Find proteins for A0A399WQY8 (Armatimonadota bacterium)
Explore A0A399WQY8 
Go to UniProtKB:  A0A399WQY8
Entity Groups  
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UniProt GroupA0A399WQY8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*CP*CP*AP*G)-3')B [auth C]12Armatimonadota bacterium
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (30-MER)C [auth D]30Armatimonadota bacterium
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (174-MER)D [auth B]174Armatimonadota bacterium
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 2.0: 2023-03-22
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Data processing, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-03-29
    Changes: Database references