22FN | pdb_000022fn

Cryo-EM structure of AsCas12a in complex with crDNA and RNA target

• PDB DOI: https://doi.org/10.2210/pdb22FN/pdb
• NAKB: 22FN
• EM Map EMD-68245: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct, Acidaminococcus sp. BV3L6
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2026-01-08 Released: 2026-04-29 
• Deposition Author(s): Lam, W.H., Wu, X., Hsing, I.M., Zhai, Y.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

DNA-guided CRISPR-Cas12a effectors for programmable RNA recognition and cleavage.

Wu, X., Lam, W.H., Zhao, Z., Cao, Y., Lin, H., Feng, X., Zhai, Y., Hsing, I.M.

(2026) Nat Biotechnol 

• PubMed: 42067668 
• DOI: https://doi.org/10.1038/s41587-026-03120-5
• Primary Citation Related Structures: 
  22FN


• PubMed Abstract: 
  

  CRISPR-Cas effectors typically rely on RNA guides to recognize target sequences. In Cas12a, the protospacer adjacent motif on DNA engages conserved protein residues, triggering target binding and nuclease activation. Here we reprogram Cas12a into a DNA-guided, RNA-targeting effector. Exploiting protospacer-adjacent motif-dependent interaction, we engineer synthetic CRISPR DNA that engages Cas12a to form a functional deoxyribonucleoprotein complex, while repurposing solely RNA as the programmable target. Structural, biophysical and biochemical analyses reveal the molecular basis of this DNA-guided, RNA-targeting configuration and support an activation pathway distinct from that of canonical RNA-guided systems. DNA-guided Cas12a enables direct RNA detection and efficient intracellular RNA knockdown, establishing a modular activation architecture for CRISPR-Cas12a and expanding the design space for programmable RNA manipulation.

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Organizational Affiliation: 
• Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China.
Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 178.94 kDa 
• Atom Count: 11,105 
• Modeled Residue Count: 1,266 
• Deposited Residue Count: 1,395 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas12a	B [auth A]	1,307	Acidaminococcus sp. BV3L6	Mutation(s): 2  Gene Names: cas12a, cpf1, HMPREF1246_0236 EC: 3.1.21.1 (PDB Primary Data), 4.6.1.22 (PDB Primary Data)
UniProt
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6)) Explore U2UMQ6  Go to UniProtKB:  U2UMQ6

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*AP*CP*AP*GP*CP*CP*CP*AP*CP*AP*UP*GP*GP*CP*AP*UP*UP*CP*CP*AP*CP*U)-3')	A [auth B]	45	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (41-MER)	C	43	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.7.1
MODEL REFINEMENT	PHENIX	1.21.2-5419-000

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-29 
Deposition Author(s): Lam, W.H., Wu, X., Hsing, I.M., Zhai, Y.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	--

Revision History  

• Version 1.0: 2026-04-29
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Data collection, Database references