9YLX | pdb_00009ylx

Cryo-EM structure of the CbCash filament bound to cA4

• PDB DOI: https://doi.org/10.2210/pdb9YLX/pdb
• EM Map EMD-73096: EMDB EMDataResource
• NAKB: 9YLX

• Classification: RNA BINDING PROTEIN
• Organism(s): Chloroflexia, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-09 Released: 2026-04-29 
• Deposition Author(s): Liu, Y., Weickert, P., Strecker, J.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Prokaryotic Schlafen proteins cleave tRNAs during type III CRISPR immunity.

Weickert, P., Liu, Y., Strecker, J.

(2026) Nat Commun 

• PubMed: 42393087 
• DOI: https://doi.org/10.1038/s41467-026-74880-6
• Primary Citation Related Structures: 
  9YLU, 9YLV, 9YLX


• PubMed Abstract: 
  

  Schlafen nucleases restrict viral infection in mammals by cleaving self RNAs, however, their function and mechanism in prokaryotic immunity is unknown. Here, we uncover CRISPR-associated Schlafen (Cash) proteins containing a Schlafen domain fused to Csx15, an uncharacterized member of Rossmann-like nucleotide-binding sensors. Cash is activated by cyclic tetra-adenylate (cA₄) produced during type III CRISPR interference and induces cell toxicity by cleaving tRNAs, primarily in the T-loop. Cryo-electron microscopy structures of Chloroflexi bacterium Cash reveal an inactive dodecamer, the formation of a filament upon cA₄ binding to align catalytic interfaces, and the molecular basis of substrate recognition and cleavage in a tRNA-bound complex. We identify numerous families of prokaryotic Schlafen proteins associated with diverse antiviral defense systems and characterized by unique sensor domains. This work highlights tRNA depletion by Schlafen nucleases as an evolutionary recurring antiviral strategy and reveals mechanistic differences between Cash and human Schlafen members.

---

Organizational Affiliation: 
• Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
Department of Genetics, Harvard Medical School, Boston, MA, USA.
Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. [e-mail].
Department of Genetics, Harvard Medical School, Boston, MA, USA. [e-mail].
Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 273.33 kDa 
• Atom Count: 18,958 
• Modeled Residue Count: 2,365 
• Deposited Residue Count: 2,392 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CbCash	A, B, C, D, E, F, G, H	297	Chloroflexia	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Cyclic tetraadenylate	I, J, K, L	4	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.45 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	cryoSPARC	4.6.1
RECONSTRUCTION	cryoSPARC	4.6.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-29 
Deposition Author(s): Liu, Y., Weickert, P., Strecker, J.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-04-29
  Type: Initial release
  
• Version 1.1: 2026-07-15
  Changes: Data collection, Database references