9WXI | pdb_00009wxi

Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the post-cleavage state

• PDB DOI: https://doi.org/10.2210/pdb9WXI/pdb
• EM Map EMD-66347: EMDB EMDataResource
• NAKB: 9WXI

• Classification: IMMUNE SYSTEM
• Organism(s): Gammaproteobacteria bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-25 Released: 2026-06-24 
• Deposition Author(s): Mitsuda, Y., Ishikawa, J., Nagahata, N., Hiraizumi, M., Yamashita, K., Nishimasu, H.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanism of SAM-AMP and SAM-AMP 2 synthesis by the type III-D2 CRISPR effector complex.

Mitsuda, Y., Sugaya, M., Ishikawa, J., Nagahata, N., Okazaki, S., Hiraizumi, M., Kato, K., Gootenberg, J.S., Abudayyeh, O.O., Osawa, T., Yamashita, K., Nishimasu, H.

(2026) Nat Commun 17

• PubMed: 42342668 
• DOI: https://doi.org/10.1038/s41467-026-74422-0
• Primary Citation Related Structures: 
  9WXH, 9WXI, 9WXJ


• PubMed Abstract: 
  

  The type III-D2 CRISPR-Cas system comprises multiple Cas subunits and a CRISPR RNA, and is likely an evolutionary intermediate between the well-studied type III-A and III-E systems. Here we show that the type III-D2 complex synthesizes two distinct second messengers, SAM-AMP and SAM-AMP ₂ , from S-adenosylmethionine (SAM) and ATP in response to target RNA recognition. We determined cryo-electron microscopy structures of the type III-D2 effector complex in different functional states, providing mechanistic insights into target RNA cleavage and second messenger synthesis. The structures reveal how SAM and ATP are recognized by the Cas10 subunit within the effector complex. Furthermore, our biological data suggest that both SAM-AMP and SAM-AMP ₂ act on the CorA ancillary effector, inducing growth arrest of infected bacterial cells and thereby conferring immunity. Thus, our study establishes the type III-D2 system as a unique anti-phage defense mechanism that employs both SAM-AMP and SAM-AMP ₂ as second messengers, expanding the repertoire of second messenger strategies in bacterial defense systems and highlighting the remarkable functional diversity of CRISPR-Cas systems.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan.
Mechanistic Immunology Research Unit, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
Department of Medicine, Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA.
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan. [e-mail].
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan. [e-mail].
Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 302.04 kDa 
• Atom Count: 19,532 
• Modeled Residue Count: 2,348 
• Deposited Residue Count: 2,537 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas10	B	592	Gammaproteobacteria bacterium	Mutation(s): 0  Gene Names: ENJ84_12795

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR type III-associated protein domain-containing protein	C	635	Gammaproteobacteria bacterium	Mutation(s): 0  Gene Names: ENJ84_12800

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TIGR03986 family CRISPR-associated RAMP protein	D	1,235	Gammaproteobacteria bacterium	Mutation(s): 0  Gene Names: ENJ84_12805

Entity ID: 1
Molecule	Chains	Length	Organism	Image
CRISPR RNA	A	43	Gammaproteobacteria bacterium

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Cleaved cognate target RNA (CTR)	E	32	Gammaproteobacteria bacterium

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SAM (Subject of Investigation/LOI)	H [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN (Subject of Investigation/LOI)	I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Mitsuda, Y., Ishikawa, J., Nagahata, N., Hiraizumi, M., Yamashita, K., Nishimasu, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR23B6
Japan Society for the Promotion of Science (JSPS)	Japan	25H00436

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Data collection, Database references