A Passage Through the Ribosome by Cryo-EM - Biophysical Approaches to Translational Control of Gene Expression - page 38

Fig. 2.4 Comparison of the
binding positions of RbfA
and Era on the 30S Subunit:
( a ) Binding position of RbfA
( red ) and Era ( magenta ;
Sharma et al. 2005 ) on the
30S subunit. ( b ) RbfA ( red )
and Era ( magenta ) interact
with a common structural
element, h28, of the 16S
rRNA ( cyan ). The thumbnail
to the left depicts the
orientation of the 30S
subunit. Source : Fig “No. 7”
from the following reference
Datta et al. ( 2007 )

a

h28

Era

RbfA

b

Era

h28

RbfA

p

h

C

h27

h1

bk

b

processed efficiently to 16S rRNA. Thus it was important to investigate how RbfA
was working. Even after several try crystallization of 30S RbfA was not possible by

a Japanese research group (personal communication) which led Datta et al. ( 2007 )
to study the 30S

⋅

RbfA cryo-
EM map through molecular docking showed that RbfA bound to the 30S subunit in
a position overlapping to the binding sites of the A- and P-site tRNAs, and RbfA's
functionally important C terminus extended toward the 5¢ end of the 16S rRNA,
which could provide stability to form the canonical helix 1. It also revealed that
binding of RbfA displaced a portion of the 16S rRNA encompassing helix 44 and 45
from its consensus position of a matured 30S. Those portions of 16S rRNA are
known to be directly involved in mRNA decoding and tRNA binding. From bio-
chemical study it was known that over-expression of Era could functionally comple-
ment the function of RbfA (i.e., providing stability to the h1) in a ΔRbfA strain
during cold-shock. Datta et al. ( 2007 ) found that portions of RbfA and Era were able
to interact to the either side of neck region of the 30S that was composed of h28. The
h28 in turn interacted with the h1, thus in the absence of RbfA the Era could provide
stability to the h1 indirectly by interacting with the h28 (see Fig. 2.4 ).

⋅ RbfA complex under cryo-EM. Analyses of the 30S ⋅