8Z40 | pdb_00008z40

The structure of type III CRISPR-associated deaminase apo form

• PDB DOI: https://doi.org/10.2210/pdb8Z40/pdb
• EM Map EMD-39759: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Limisphaera ngatamarikiensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-16 Released: 2024-12-11 
• Deposition Author(s): Chen, M.R., Li, Z.X., Xiao, Y.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Antiviral signaling of a type III CRISPR-associated deaminase.

Li, Y., Li, Z., Yan, P., Hua, C., Kong, J., Wu, W., Cui, Y., Duan, Y., Li, S., Li, G., Ji, S., Chen, Y., Zhao, Y., Yang, P., Hu, C., Lu, M., Chen, M., Xiao, Y.

(2025) Science 387: eadr0393-eadr0393

• PubMed: 39666823 
• DOI: https://doi.org/10.1126/science.adr0393
• Primary Citation Related Structures: 
  8Z3K, 8Z3P, 8Z3R, 8Z40


• PubMed Abstract: 
  

  Prokaryotes have evolved diverse defense strategies against viral infection, including foreign nucleic acid degradation by CRISPR-Cas systems and DNA and RNA synthesis inhibition through nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated adenosine triphosphate (ATP) depletion in which ATP is converted into inosine triphosphate (ITP) by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA ₄ or cA ₆ , followed by hydrolysis into inosine monophosphate (IMP) by Nudix hydrolase, ultimately resulting in cell growth arrest. The cryo-electron microscopy structures of CAAD in its apo and activated forms, together with biochemical evidence, revealed how cA ₄ or cA ₆ binds to the CRISPR-associated Rossmann fold (CARF) domain and abrogates CAAD autoinhibition, inducing substantial conformational changes that reshape the structure of CAAD and induce its deaminase activity. Our results reveal the mechanism of a CRISPR-Cas-regulated ATP depletion antiviral strategy.

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Organizational Affiliation: 
• Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
School of Pharmacy, Hunan University of Chinese Medicine, Changsha, China.
College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China.
School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China.
Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 425.16 kDa 
• Atom Count: 21,893 
• Modeled Residue Count: 2,810 
• Deposited Residue Count: 3,810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase domain-containing protein	A, B, C, D, E, F	635	Limisphaera ngatamarikiensis	Mutation(s): 0  Gene Names: G4L39_03315 EC: 3.5.4.4
UniProt
Find proteins for A0A6M1RED6 (Limisphaera ngatamarikiensis) Explore A0A6M1RED6  Go to UniProtKB:  A0A6M1RED6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 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: 2024-12-11 
Deposition Author(s): Chen, M.R., Li, Z.X., Xiao, Y.B.

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

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Data collection, Database references
• Version 1.2: 2025-03-05
  Changes: Data collection, Database references
• Version 1.3: 2025-07-23
  Changes: Data collection, Database references