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S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, B.P.Klaholz. (2007). Structured mRNAs regulate translation initiation by binding to the platform of the ribosome. Cell, 130, 1019-1031. [PubMed id: 17889647]
Figure 4.
Figure 4. The Platform-Binding Center for Folded 5′-UTR mRNAs
The platform-binding center for structured mRNAs is shown on the small ribosomal subunit (Schuwirth et al., 2005) (viewing angle as in Figure 3 top panel). Ribosomal proteins and RNA helices are labeled and color-coded as in Figure 3. Conserved surface residues of S2, S7, and S11, adjacent to the position of the folded mRNAs, are highlighted by cyan van der Waals spheres. In the case of the rspO-S15 complex, a conformational change positions S2 away from helix h26 (compared to the crystal structure) providing additional conserved residues (highlighted in red) for mRNA binding.
Figure 5.
Figure 5. Schematic Representation of the Entrapment Mechanism and Its Relief
Comparison of the folded rpsO mRNA position (A) with the normal mRNA path (B) obtained after S15 release and fMet-tRNA^fMet binding. The 50S (orange) and the 30S (light blue) subunits are represented as a projection shape seen from the top of the ribosome. In the active 70S initiation complex (B), the initiation codon is located in the P-site and interacts with the fMet-tRNA^fMet (Yusupova et al., 2001). In the inactive 70S complex (A), repressor protein S15 stabilizes the rpsO mRNA in a folded conformation and prevents the start codon from entering the mRNA channel. The SD sequence of the mRNA (in magenta) interacts with the anti-SD sequence at the 3′ end of the 16S rRNA (in orange) forming a short helix, which is shifted outwards in the 70S-rpsO-S15 complex. SD/anti-SD interactions are present in the docked and unfolded states.
Figures reprinted by permission from Cell Press: Cell (2007, 130, 1019-1031) copyright 2007.
PDB entries for which this is a key reference: 2vaz.
M.J.Macias, V.Gervais, C.Civera, H.Oschkinat. (2000). Structural analysis of WW domains and design of a WW prototype. Nat Struct Biol, 7, 375-379. [PubMed id: 10802733]
Figure 2.
Figure 2. Pattern of secondary structure NOEs observed for Yap65WW (black), FBP28WW (green), YJQ8WW (red) and the WW prototype (blue). Arrows with asterisks denote undetected NOEs in the spectra of YJQ8WW. Hydrogen bonds (orange dotted lines) correspond to slow 2H[2]O/H[2]O exchanging amides of Yap65WW and FBP28WW. Residue numbers correspond to the constructs used for the structural studies. For the Yap65WW sequence, residue numbers are as in the published structure^7.
Figure 3.
Figure 3. Structures of the a, FBP28WW, b, YJQ8WW, and c, WW prototype domains. Stereo views showing the backbone superposition of 10 NMR structures selected on the basis of minimal total energy for FBP28WW (green), YJQ8WW (red) and the WW prototype (blue) are shown on the left. Selected conserved residues are shown in blue. Cartoon representations of the minimal energy structures are shown on the right.
Figures reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 375-379) copyright 2000.
PDB entries for which this is a key reference: 1e0l, 1e0m, 1e0n.
N.Shibata, T.Inoue, K.Fukuhara, Y.Nagara, R.Kitagawa, S.Harada, N.Kasai, K.Uemura, K.Kato, A.Yokota, Y.Kai. (1996). Orderly disposition of heterogeneous small subunits in D-ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach. J Biol Chem, 271, 26449-26452. [PubMed id: 8900108]
Figure 2.
Fig. 2. Two-dimensional gel electrophoresis of purified spinach Rubisco. LSU and SSU indicate the L and S peptides, respectively. The stained gel between pI 5.88 and 6.60 is shown in the figure.
Figure 3.
Fig. 3. Schematic drawing of the L[8]SI[4]SII[4] structure. The SI and SII subunits are shown as green and yellow stick models, respectively. The white dots show the C atoms of the eight large subunits. There are three 2-fold axes in the spinach Rubisco molecule; one of them corresponds to a crystallographic axis (red), and the others are noncrystallographic axes (white). This drawing was prepared using MidasPlus (30).
Figures reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 26449-26452) copyright 1996.
PDB entries for which this is a key reference: 1bur.
B.H.Sandler, L.Nikonova, W.S.Leal, J.Clardy. (2000). Sexual attraction in the silkworm moth: structure of the pheromone-binding-protein-bombykol complex. Chem Biol, 7, 143-151. [PubMed id: 10662696]
Figure 6.
Figure 6. Another view of the bombykol binding pocket of B. mori PBP. Bombykol is at the center of the figure in ball-and-stick representation. The hydroxyl group is red, and the double bonds are green. Residues surrounding bombykol are shown in stick representation. Red denotes residues highly conserved across lepidopteran PBPs and GOBPs, residues in orange are conserved across PBPs but not GOBPs, and residues in yellow are the least conserved among lepidopteran PBPs. The figure was prepared using BOBSCRIPT [36, 37 and 38].
Figure 7.
Figure 7. Close-up view of the loop covering the binding pocket. Sidechains are shown only for select residues (Asp63, Pro64, Glu65, His69, His70, His95 and Glu98). Hydrogen bonds are shown as dashed lines. The figure was prepared using BOBSCRIPT [36, 37 and 38].
Figures reprinted by permission from Cell Press: Chem Biol (2000, 7, 143-151) copyright 2000.
PDB entries for which this is a key reference: 1dqe.
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