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

• 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 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.

To be published.

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