7YOJ | pdb_00007yoj

Structure of CasPi with guide RNA and target DNA

• PDB DOI: https://doi.org/10.2210/pdb7YOJ/pdb
• EM Map EMD-33983: EMDB EMDataResource
• NAKB: 7YOJ

• Classification: RNA BINDING PROTEIN/DNA/RNA
• Organism(s): Armatimonadota bacterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-08-01 Released: 2023-02-15 
• Deposition Author(s): Li, C.P., Wang, J., Liu, J.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

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

• PubMed: 36650285 
• DOI: https://doi.org/10.1038/s41422-022-00771-2
• Primary Citation 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.

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Organizational Affiliation: 
• Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
Department of Environmental Engineering, Peking University, Beijing, China.
Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, China.
Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 168.02 kDa 
• Atom Count: 11,545 
• Modeled Residue Count: 1,083 
• Deposited Residue Count: 1,083 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CasPi	A	867	Armatimonadota bacterium	Mutation(s): 2  Gene Names: DCC45_12200, EDM73_08925
UniProt
Find proteins for A0ACD6B9Z5 (Armatimonadota bacterium) Explore A0ACD6B9Z5  Go to UniProtKB:  A0ACD6B9Z5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*CP*CP*AP*G)-3')	B [auth C]	12	Armatimonadota bacterium

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (30-MER)	C [auth D]	30	Armatimonadota bacterium

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (174-MER)	D [auth B]	174	Armatimonadota bacterium

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Li, C.P., Wang, J., Liu, J.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• 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
• Version 2.2: 2024-07-03
  Changes: Data collection