8D4B | pdb_00008d4b

Structure of Cas12a2 ternary complex

• PDB DOI: https://doi.org/10.2210/pdb8D4B/pdb
• EM Map EMD-27180: EMDB EMDataResource
• NAKB: 8D4B

• Classification: DNA Binding Protein/RNA
• Organism(s): Sulfuricurvum sp. PC08-66, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-01 Released: 2023-01-18 
• Deposition Author(s): Bravo, J.P.K., Taylor, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2.

Bravo, J.P.K., Hallmark, T., Naegle, B., Beisel, C.L., Jackson, R.N., Taylor, D.W.

(2023) Nature 613: 582-587

• PubMed: 36599980 
• DOI: https://doi.org/10.1038/s41586-022-05560-w
• Primary Citation Related Structures: 
  8D49, 8D4A, 8D4B


• PubMed Abstract: 
  

  Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided, sequence-nonspecific degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA following recognition of a complementary RNA target, culminating in abortive infection ¹ . Here we report structures of Cas12a2 in binary, ternary and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of 'aromatic clamp' residues that are crucial for double-stranded DNA degradation and in vivo immune system function. Our work provides a structural basis for this mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.

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Organizational Affiliation: 
• Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA.
Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
Medical Faculty, University of Würzburg, Würzburg, Germany.
Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA. [e-mail].
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. [e-mail].
Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA. [e-mail].
Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA. [e-mail].
LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, USA. [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: 165.26 kDa 
• Atom Count: 11,010 
• Modeled Residue Count: 1,235 
• Deposited Residue Count: 1,301 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OrfB_Zn_ribbon domain-containing protein	A	1,232	Sulfuricurvum sp. PC08-66	Mutation(s): 0  Gene Names: KU37_03970
UniProt
Find proteins for A0ACD6B9W3 (Sulfuricurvum sp. PC08-66) Explore A0ACD6B9W3  Go to UniProtKB:  A0ACD6B9W3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (41-MER)	B	41	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (28-MER)	C	28	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Bravo, J.P.K., Taylor, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138348
Welch Foundation	United States	F-1938
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR160088

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2024-06-12
  Changes: Data collection
• Version 1.3: 2025-06-04
  Changes: Data collection, Structure summary