Chloroplasts contain a unique signal recognition particle (cpSRP). Unlike the 
cytoplasmic forms, the cpSRP lacks RNA but contains a conserved 54-kDa GTPase 
and a novel 43-kDa subunit (cpSRP43). Recently, three functionally distinct 
chromodomains (CDs) have been identified in cpSRP43. In the present study, we 
report the three-dimensional solution structures of the three CDs (CD1, CD2, and 
CD3) using a variety of triple resonance NMR experiments. The structure of CD1 
consists of a triple-stranded beta-sheet segment. The C-terminal helical segment 
typically found in the nuclear chromodomains is absent in CD1. The secondary 
structural elements in CD2 and CD3 include a triple-stranded antiparallel 
beta-sheet and a C-terminal helix. Interestingly, the orientation of the 
C-terminal helix is significantly different in the structures of CD2 and CD3. 
Critical comparison of the structures of the chromodomains of cpSRP43 with those 
found in nuclear chromodomain proteins revealed that the diverse protein-protein 
interactions mediated by the CDs appear to stem from the differences that exist 
in the surface charge potentials of each CD. Results of isothermal titration 
calorimetry experiments confirmed that only CD2 is involved in binding to 
cpSRP54. The negatively charged C-terminal helix in CD2 possibly plays a crucial 
role in the cpSRP54-cpSRP43 interaction.