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A random selection of article figures used in PDBsum

The 4 randomly selected references below show some of the article figures used in PDBsum. Each reference may relate to one or more PDBsum entries and may be one of the following types:
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  • secondary reference - listed in the REMARK records of the corresponding PDB file, or
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Y.Kurakata, A.Uechi, H.Yoshida, S.Kamitori, Y.Sakano, A.Nishikawa, T.Tonozuka. (2008). Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63. J Mol Biol, 381, 116-128. [PubMed id: 18586271]
Figure 1.
Fig. 1. Three-dimensional structures of YgjK and structurally homologous proteins. The figures were generated using PyMol. (a) Overall structure of YgjK shown as a ribbon model. The N-domain, A-domain, and linker region are in blue, green, and orange, respectively. The A′-region contained in the A-domain is shown in magenta. One calcium molecule is shown as a yellow sphere, and two glycerol molecules are in black. (b) A side view of YgjK. The orientation is rotated 90° counterclockwise from that of (a). (c) Structure of tGA glucoamylase. The β-domain, α-domain, and linker domain are in blue, green, and orange, respectively. (d) Structure of V. proteolyticus ChBP. The N-terminal domain, linker helices, α-helical domain, and C-terminal domain are in blue, orange, green, and pink, respectively. The calcium ions are shown as yellow spheres.
Figure 5.
Fig. 5. Structural comparison of YgjK, ChBP, and tGA. The figures were generated using PyMol. YgjK, ChBP, and tGA are in green, orange, and cyan, respectively. (a) Superposition of the structurally conserved crucial residues for ChBP and tGA activity and the corresponding residues of YgjK. The residues are shown as a ball-and-stick model, and the labels correspond (from top to bottom) to YgjK, ChBP, and tGA. (b) Comparison of the A′-region of YgjK and the corresponding regions of ChBP and tGA. Asp501 of YgjK, Asp492 of ChBP, and Glu438 of tGA are shown as ball-and-stick models. The structures are superposed based on the C^α atoms of AH5 and AH6 of YgjK and the corresponding helices of ChBP and tGA.
Figures reprinted by permission from Elsevier: J Mol Biol (2008, 381, 116-128) copyright 2008.
PDB entries for which this is a key reference: 3c67, 3c68, 3c69, 3d3i, 3w7s, 3w7t, 3w7u.
G.Z.Yusupova, M.M.Yusupov, J.H.Cate, H.F.Noller. (2001). The path of messenger RNA through the ribosome. Cell, 106, 233-241. [PubMed id: 11511350]
Figure 1.
Figure 1. Nucleotide Sequences of the Three Model mRNAs Used in this StudyThe Shine-Dalgarno sequence (S/D), and P- and A-site codons are underlined. The self-complementary sequences forming the putative A-site helix in MF36 mRNA are overlined
Figure 2.
Figure 2. Fourier Difference Maps of mRNAs(A) 7 Å Fourier difference map of MK27 mRNA with the mRNA model (yellow) docked, showing the position of the Shine-Dalgarno (S/D) helix (magenta) and the positions of the A- and P-site codons (orange and red, respectively), viewed from the top of the 30S ribosomal subunit.(B) Difference map of the MF36 mRNA, showing a four-base-pair tetraloop helix (A-site helix) fitted to the extra density at the A site.(C) Same as for (B), except that the A-tRNA anticodon stem-loop (green) is shown in the position observed experimentally in the A-tRNA difference map (Yusupov et al., 2001), in place of the A-site mRNA helix. The five-nucleotide (GGAGG/CCUCC) core of the Shine-Dalgarno interaction is shown in magenta, and the rest of the 16S rRNA tail in cyan
Figures reprinted by permission from Cell Press: Cell (2001, 106, 233-241) copyright 2001.
PDB entries for which this is a key reference: 1jgo, 1jgp, 1jgq.
PDB entries for which this is a secondary reference: 1mvr.
P.H.Carter, P.A.Scherle, J.K.Muckelbauer, M.E.Voss, R.Q.Liu, L.A.Thompson, A.J.Tebben, K.A.Solomon, Y.C.Lo, Z.Li, P.Strzemienski, G.Yang, N.Falahatpisheh, M.Xu, Z.Wu, N.A.Farrow, K.Ramnarayan, J.Wang, D.Rideout, V.Yalamoori, P.Domaille, D.J.Underwood, J.M.Trzaskos, S.M.Friedman, R.C.Newton, C.P.Decicco, J.A.Muckelbauer. (2001). Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha. Proc Natl Acad Sci U S A, 98, 11879-11884. [PubMed id: 11592999]
Figure 1.
Fig. 1. Chemical structures of some optimized TNF- inhibitors.
Figure 6.
Fig. 6. Superimposition of the crystal structures of IV703 bound to TNFRc1 (purple, this study) and that of TNF- bound to TNFRc1 (green; ref. 11). Note that Tyr-108 (TNF- ) normally interacts with Ala-62 (TNFRc1) (11); this receptor residue is bound to IV703 in our structure.
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2001, 98, 11879-11884) copyright 2001.
PDB entries for which this is a key reference: 1ft4.
A.B.Conway, Y.Chen, P.A.Rice. (2003). Structural plasticity of the Flp-Holliday junction complex. J Mol Biol, 326, 425-434. [PubMed id: 12559911]
Figure 5.
Figure 5. Two forms of the active site. (a) Closeup of the active site of the purple protomer (as colored in Figure 2 and Figure 4), showing Y343 from the red protomer covalently linked to the 3' phosphate group of the DNA. (b) In the inactive catalytic centers, the DNA strand is continuous, and Y343 is disordered in one case and ordered but adjacent to the wrong phosphate group in the other case.
Figure 6.
Figure 6. Comparison of type I and type II interfaces. Colors are the same as in Figure 2(c), with the new structure in dark tones and the previously reported structure superimposed in pastel colors. The catalytic domains are below the DNA in this orientation. (a) In a type I interaction, the green protomer donates its nucleophilic tyrosine residue (yellow) to the active site of the purple protomer. (b) In a type II interaction, the helix bearing the nucleophilic tyrosine residue from the red protomer is pulled away from the red protomer and is disordered. Comparison of the two crystal forms shows that this interface is quite flexible.
Figures reprinted by permission from Elsevier: J Mol Biol (2003, 326, 425-434) copyright 2003.
PDB entries for which this is a key reference: 1m6x.