Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Molecular basis of SAM-AMP synthesis and degradation in the type III-B CRISPR-Cas system.
Journal, issue, pages	Nat Chem Biol, Year 2025
Publish date	Nov 21, 2025
Authors	Benzhen Duan / Xiaohui Jin / Xiaoman An / Yang Xiao / Qianxi Yang / Hongyu Zhao / Yunxiao Huang / Jingwen Wang / Qian Wang / Fenglei Du / Lu Lu / Lei Sun / Zhenguo Chen / Baoyu Zhao /
PubMed Abstract	Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers ...Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers immune responses. SAM-AMP can be degraded by NrN and SAM lyase, potentially deactivating the system. Here we find that the type III-B effector complex from Bacteroides fragilis uses a specific mechanism to recognize nonself target RNA and synthesize SAM-AMP. The 3' anti-tag of nonself target RNA induces conformational changes in the Cmr2 subunit, triggering SAM-AMP synthesis independently of the stalk loop of Cmr3 subunit. SAM-AMP binding induces NrN to transit from an open to a closed conformation, enabling hydrolysis of the 3'-5' phosphodiester bond. SAM lyase forms a triangular trimer that specifically degrades SAM-AMP into 5'-methylthioadenosine-AMP and homoserine lactone. These findings unveil unique mechanisms for SAM-AMP synthesis and degradation and provide deeper insights into the molecular basis of type III CRISPR-Cas signaling.
External links	Nat Chem Biol / PubMed:41272318
Methods	EM (single particle) / X-ray diffraction
Resolution	1.28 - 2.97 Å
Structure data	63293 9lq5 EMDB-63293, PDB-9lq5: Cryo-EM structure of Apo type III-B CRISPR-Cas effector complex Method: EM (single particle) / Resolution: 2.97 Å 63294 9lq6 EMDB-63294, PDB-9lq6: Cryo-EM structure of adTR-bound type III-B CRISPR-Cas effector complex Method: EM (single particle) / Resolution: 2.94 Å 63295 9lq7 EMDB-63295, PDB-9lq7: Cryo-EM structure of NTR-bound type III-B CRISPR-Cas effector complex Method: EM (single particle) / Resolution: 2.81 Å 63296 9lq8 EMDB-63296, PDB-9lq8: Cryo-EM structure of CTR-bound type III-B CRISPR-Cas effector complex Method: EM (single particle) / Resolution: 2.85 Å PDB-9lq9: Crysral structure of NrN Method: X-RAY DIFFRACTION / Resolution: 2.38 Å PDB-9lqa: Crystal structure of NrN E21A in complex with SAM-AMP Method: X-RAY DIFFRACTION / Resolution: 1.91 Å PDB-9lqb: Crystal structure of NrN E21A in complex with SAH-AMP Method: X-RAY DIFFRACTION / Resolution: 1.93 Å PDB-9lqc: Crystal structure of NrN D119A in complex with SAH-AMP Method: X-RAY DIFFRACTION / Resolution: 2.37 Å PDB-9lqd: Crystal structure of SAM lyase Method: X-RAY DIFFRACTION / Resolution: 2.16 Å PDB-9lqe: Crystal structure of SAM lyase in complex with SAH Method: X-RAY DIFFRACTION / Resolution: 1.94 Å PDB-9lqf: Crystal structure of SAM lyase in complex with SAH-AMP Method: X-RAY DIFFRACTION / Resolution: 1.59 Å PDB-9lqg: Crystal structure of SAM lyase in complex with MTA-AMP Method: X-RAY DIFFRACTION / Resolution: 1.28 Å PDB-9lqh: Crystal structure of SAM lyase in complex with sinefungin-AMP Method: X-RAY DIFFRACTION / Resolution: 1.47 Å
Chemicals	ChemComp-MN: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-SAM: S-ADENOSYLMETHIONINE ChemComp-HOH: WATER PDB-1el3: HUMAN ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH bufferYM PDB-1el0: SOLUTION STRUCTURE OF THE HUMAN CC CHEMOKINE, I-309 ChemComp-MLT: D-MALATE ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE ChemComp-GOL: GLYCEROL PDB-1ijb: The von Willebrand Factor mutant (I546V) A1 domain PDB-1el1: X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE)
Source	bacteroides fragilis (bacteria) clostridium botulinum (strain hall / atcc 3502 / nctc 13319 / type a) (bacteria)
Keywords	IMMUNE SYSTEM/RNA / CRISPR-Cas complex / adaptive immunity / RNA degradation / second messenger / IMMUNE SYSTEM-RNA complex / IMMUNE SYSTEM / enzyme / phosphodiesterase / CRISPR-Cas system / SAM