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PDBsum entry 2zkr

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Top Page protein dna_rna ligands Protein-protein interface(s) links
Ribosomal protein/RNA PDB id
2zkr
Jmol
Contents
Protein chains
244 a.a.
345 a.a.
257 a.a.
165 a.a.
175 a.a.
120 a.a.
48 a.a.
166 a.a.
74 a.a.
136 a.a.
124 a.a.
122 a.a.
175 a.a.
236 a.a.
120 a.a.
159 a.a.
13 a.a.
96 a.a.
150 a.a.
78 a.a.
110 a.a.
53 a.a.
61 a.a.
158 a.a.
80 a.a.
60 a.a.
58 a.a.
72 a.a.
51 a.a.
48 a.a.
92 a.a.
210 a.a.
113 a.a.
DNA/RNA
Ligands
ALA-ARG-VAL-LEU-
THR-VAL-ILE-ASN-
GLN-THR

References listed in PDB file
Key reference
Title Structure of the mammalian 80s ribosome at 8.7 a resolution.
Authors P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, C.W.Akey.
Ref. Structure, 2008, 16, 535-548. [DOI no: 10.1016/j.str.2008.01.007]
PubMed id 18400176
Abstract
In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.
Figure 2.
Figure 2. A Model of the Cytoplasmic 80S Ribosome
(A) A model of the canine ribosome is shown within a density map of the ribosome-channel complex. The E site tRNA is shown in red between the small (ssu) and large subunits (lsu) of the ribosome. This specimen contained part of the ER translocon (in magenta) that is composed of Sec61 and TRAP. The latter has a prominent lumenal domain (LD).
(B) A molecular model of the canine ribosome is shown in a front view. The subunit rRNAs and conserved proteins are color coded (see boxes). Novel proteins (spheres and rods) and expansion segments (red helices) are also included.
(C) The model of a canine ribosome is shown in a reverse view within the electron microscopy (EM) density map. The position of the ER membrane is indicated by dashed lines.
(D) The molecular model of the canine ribosome is shown in a reverse view.
Figure 7.
Figure 7. Intersubunit Bridges in the Canine Ribosome
(A) Known rotations of the body and head of the small subunit are indicated by arrows on the canine ribosome. Positions of the bridges specific to eukaryotic ribosomes and bridge 2e are indicated.
(B) A reverse view of the ribosome shows that the ebs form a contiguous line along the lateral edge of the small subunit and are also present beneath the subunits (eb11).
(C) An unmodeled C-terminal extension of L37ae contacts h22 in bridge 2e.
(D) An α helix originates from S-IV and extends across the subunit interface to form eb8. Additional density from L7ae and ES31 helps to form this bridge near the L1 stalk helix (H76).
(E) Bridge 9 (eb9) involves extensive interactions between L30e and S13e. The N-terminal helix of S13e is flipped out to interact with protein S-IX.
(F) Protein S-VII forms a bridge between ES3^S and ES41. An icon view in the lower left shows the proximity of eb11 and eb12.
(G) A C-terminal extension of L19e forms a long helix that crosses the intersubunit gap to interact with one branch of ES6^S.
The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 535-548) copyright 2008.
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