9WXH | pdb_00009wxh

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

PDB DOI: https://doi.org/10.2210/pdb9WXH/pdb
EM Map EMD-66346: EMDB EMDataResource
NAKB: 9WXH

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 307.02 kDa
Atom Count: 20,118
Modeled Residue Count: 2,392
Deposited Residue Count: 2,552
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cas10	B	592	Gammaproteobacteria bacterium	Mutation(s): 0 Gene Names: ENJ84_12795
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
CRISPR RNA	A	43	Gammaproteobacteria bacterium
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
Cognate target RNA (CTR)	E	47	Gammaproteobacteria bacterium
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], H [auth B], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C]