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PDBsum entry 2r1c
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RNA binding protein
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PDB id
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2r1c
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References listed in PDB file
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Key reference
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Title
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Structural aspects of rbfa action during small ribosomal subunit assembly.
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Authors
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P.P.Datta,
D.N.Wilson,
M.Kawazoe,
N.K.Swami,
T.Kaminishi,
M.R.Sharma,
T.M.Booth,
C.Takemoto,
P.Fucini,
S.Yokoyama,
R.K.Agrawal.
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Ref.
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Mol Cell, 2007,
28,
434-445.
[DOI no: ]
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PubMed id
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Abstract
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Ribosome binding factor A (RbfA) is a bacterial cold shock response protein,
required for an efficient processing of the 5' end of the 16S ribosomal RNA
(rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a
crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional
cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to
the 30S subunit in a position overlapping the binding sites of the A and P site
tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of
the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing
helix 44, which is known to be directly involved in mRNA decoding and tRNA
binding, is displaced. These results shed light on the role played by RbfA
during maturation of the 30S subunit, and also indicate how RbfA provides cells
with a translational advantage under conditions of cold shock.
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Figure 1.
Figure 1. Crystal Structure of Tth RbfA and Its Comparison
with Known Atomic Structures of RbfA from Other Species
(A)
Stereo representation of the Tth RbfA is shown in cartoon (PDB
ID, 2DYJ).
(B) An enlarged view of the helix-kink-helix
motif (cyan) with all residues in stick. Residues involved in
notable interactions, Asp25 and Arg27 on the 3[10] helix
(magenta) and the conserved Phe87, are also shown in stick.
(C) Stereo representation of Tth RbfA in the surface potential
prepared by using APBS tools built in PyMOL.
(D)
Superposition of structures of RbfA from T. Thermophilus
(molecules A and B in the asymmetric unit are shown in dark and
light blue colors, respectively), H. influenzae (green, 1JOS),
and M. pneumoniae (orange, 1PA4). In all panels, N, C, and hkh
mean N terminus, C terminus, and helix-kink-helix motif,
respectively.
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Figure 7.
Figure 7. 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.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Mol Cell
(2007,
28,
434-445)
copyright 2007.
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