A protein-RNA complex orchestrated by EMB1006, EMB1270, EMB976, and CFM2 facilitates clpP1 intron 2 splicing in Arabidopsis chloroplasts

• EMB1006 specifically binds to a sequence near the 3′ end of clpP1 exon 2, as confirmed by RNA electrophoretic mobility shift assays guided by PPR code prediction. • Immunoprecipitation coupled with mass spectrometry reveals that EMB1006 forms a complex with EMB1270, EMB976, and CFM2. • Direct interactions between EMB1006 and EMB1270 or CFM2 are supported by yeast two-hybrid and semi-in vivo pull-down assays, while EMB976 does not directly interact with these proteins. • A model is proposed where EMB1006 and EMB1270 bind to distinct sites on clpP1 pre-mRNA and, together with CFM2 and possibly indirect association with EMB976, assemble into a protein-RNA complex that facilitates clpP1.2 splicing.