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Structure paper

TitleStructural mechanism of SAM-AMP and SAM-AMP synthesis by the type III-D2 CRISPR effector complex.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateJun 24, 2026
AuthorsYoshihisa Mitsuda / Maki Sugaya / Junichiro Ishikawa / Naoto Nagahata / Sae Okazaki / Masahiro Hiraizumi / Kazuki Kato / Jonathan S Gootenberg / Omar O Abudayyeh / Tsuyoshi Osawa / Keitaro Yamashita / Hiroshi Nishimasu /
PubMed AbstractThe 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 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, 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 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 as second messengers, expanding the repertoire of second messenger strategies in bacterial defense systems and highlighting the remarkable functional diversity of CRISPR-Cas systems.
External linksNat Commun / PubMed:42342668 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 2.9 Å
Structure data

66346

9wxh

EMDB-66346, PDB-9wxh:
Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
Method: EM (single particle) / Resolution: 2.6 Å

66347

9wxi

EMDB-66347, PDB-9wxi:
Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the post-cleavage state
Method: EM (single particle) / Resolution: 2.8 Å

66348

9wxj

EMDB-66348, PDB-9wxj:
Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a non-cognate target RNA in the pre-cleavage state
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-69899: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the pre-cleavage state
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-69900: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a cognate target RNA in the post-cleavage state
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-69901: Cryo-EM structure of the type III-D2 CRISPR-Cas effector complex bound to a non-cognate target RNA in the pre-cleavage state
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-SAM:
S-ADENOSYLMETHIONINE

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • gammaproteobacteria bacterium (bacteria)
KeywordsIMMUNE SYSTEM / CRISPR / Anti-phage defense / Second messenger / SAM-AMP

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