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PDBsum entry 1ysh
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Structural protein/RNA
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PDB id
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1ysh
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References listed in PDB file
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Key reference
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Title
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Localization and dynamic behavior of ribosomal protein l30e.
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Authors
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M.Halic,
T.Becker,
J.Frank,
C.M.Spahn,
R.Beckmann.
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Ref.
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Nat Struct Mol Biol, 2005,
12,
467-468.
[DOI no: ]
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PubMed id
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Abstract
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The ribosomal protein L30e is an indispensable component of the eukaryotic 80S
ribosome, where it is part of the large (60S) ribosomal subunit. Here, we
determined the localization of L30e in the cryo-EM map of the 80S wheat germ
(wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between
large and small subunits, where it dynamically participates in the formation of
the two intersubunit bridges eB9 and B4.
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Figure 1.
Figure 1. Localization of L30e in a 9.5-Å cryo-EM map of the 80S
ribosome. (a) Cryo-EM density of the wheat germ 80S ribosome
(accession code EMD-3361 in EMBL 3D-EM database). Yellow, 40S
subunit; blue, 60S subunit; green, P-site tRNA; magenta, L30e;
SB, stalk base; CP, central protuberance. Right density is
rotated by 150°. (b) L30e as part of the isolated 60S subunit
density. SRL, sarcin ricin loop. (c) 25S RNA secondary structure
diagram of domains II and III. Magenta, L30e-binding region of
helix 58 (R.R. Gutell, University of Texas at Austin,
http://www.rna.icmb.utexas.edu).
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Figure 2.
Figure 2. Model of L30e in its ribosomal environment. (a)
Wheat germ L30e amino acid sequence with cylinders and arrows
indicating  -helical
and  -strand
secondary structure, respectively. (b) Top, L30e density at
different contour levels (2.5 and 1  ).
Bottom, adjusted homology model of L30e in transparent EM
density and L30e crystal structure (green, PDB entry, chain
D1NMUD). Note the different conformation of 4.
(c) Ribosomal environment of L30e (accession code 1YSH in the
Protein Data Bank). Blue, 25S RNA; orange, L37Ae and unknown
protein cluster II; magenta, L30e; yellow, 18S RNA; green, S13e
(S15p). Ribosome indicates orientation. (d) L30e conformation in
the post state and in the eEF2-bound state of the 80S ribosome.
The same region of the 60S subunit is shown in the post state
(left, wg ribosome, filtered to 13) and in the eEF2-bound state
(right, yeast ribosome at 12). B4 and eB9 indicate intersubunit
bridges. Note the differences in the density for 4
of L30e (magenta).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
467-468)
copyright 2005.
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