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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:
  • key reference - cited in the JRNL records in the corresponding PDB file,
  • secondary reference - listed in the REMARK records of the corresponding PDB file, or
  • added reference - either suggested by the author(s) or obtained from the journal in question (eg Acta Cryst D lists related PDB codes on its contents pages).
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N.Chen, M.A.Walsh, Y.Liu, R.Parker, H.Song. (2005). Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J Mol Biol, 347, 707-718. [PubMed id: 15769464]
Figure 3.
Figure 3. Comparison of the cap-binding pocket in apo-DcpS with those in m 7 GDP--DcpS and m 7 GpppG--DcpS. (a) Stereo view of superposition of the cap-binding pockets in the closed states of m 7 GDP--DcpS and m 7 GpppG--DcpS with that of apo-DcpS. (b) Stereo view of superposition of the cap-binding pockets in the open states of m 7 GDP--DcpS and m 7 GpppG--DcpS with that of apo-DcpS. The m 7 GMP, m 7 GDP m 7 GpppG molecules, the phosphate ion and residues involved in interactions with the nucleotides are shown as stick models. The coloring scheme is the same as that used in Figure 2.
Figure 5.
Figure 5. Solvent-accessible surface and electrostatic potential of apo-DcpS. The Figure reveals the positive electrostatic potential located in the channel between the N-terminal and C-terminal domains of apo-DcpS. m 7 GpppG of the m 7 GpppG--DcpS complex super- imposed on apo-Dcps is shown as a stick model. This Figure was produced using GRASP. 36
Figures reprinted by permission from Elsevier: J Mol Biol (2005, 347, 707-718) copyright 2005.
PDB entries for which this is a key reference: 1xml, 1xmm.
T.J.Brett, L.M.Traub, D.H.Fremont. (2002). Accessory protein recruitment motifs in clathrin-mediated endocytosis. Structure, 10, 797-809. [PubMed id: 12057195]
Figure 1.
Figure 1. Experimental Evidence for DPF, DPW, and FxDxF Motif Peptides Binding to the a-Ear(A) Ribbon representation of the a-ear showing the binding sites of the FxDxF (extended platform site) and DPW2 (distal site) peptides, with the peptides shown as CPK models.(B-E) The fit of each peptide to its corresponding simulated annealing omit electron density contoured at 2.5 s.(B) The FxDxF peptide at 2.15 resolution.(C) The DPF peptide (in P2[1]) at 1.22 resolution.(D) The DPW1 peptide at 2.0 resolution.(E) The DPW2 peptide at 2.0 resolution. The orientation of the peptides depicted in B, C, and D were achieved by superposition of the a-ear platform domain. For the DPW2 peptide in (E), the Ca coordinates were aligned with those of the DPF peptide. DPF, cyan; DPW1, steel blue; DPW2, blue-green; FxDxF, magenta.
Figure reprinted by permission from Cell Press: Structure (2002, 10, 797-809) copyright 2002.
PDB entries for which this is a key reference: 1ky6, 1ky7, 1kyd, 1kyf, 1kyu.
G.Szakonyi, J.M.Guthridge, D.Li, K.Young, V.M.Holers, X.S.Chen. (2001). Structure of complement receptor 2 in complex with its C3d ligand. Science, 292, 1725-1728. [PubMed id: 11387479]
Figure 3.
Fig. 3. Structure at the CR2-C3d interface. (A and B) Surface features of the interface area on C3d (in cyan) and CR2 molecule (in yellow). The shape of the interface of one molecule complements that of the other (prepared using GRASP). (C) Structure of the CR2 SCR2 (yellow) and C3d (cyan) complex. (D and E) The detailed interactions between CR2 (yellow) and C3d (cyan) in two angles. Dashed lines represent H-bonds between carbonyl oxygen atoms (red), nitrogen atoms (blue) of amino acid side chains or main chain, and water molecules (pink).
Figure 4.
Fig. 4. ELISA results demonstrating the relative inhibition of binding of full-length soluble CR2 at 2 µg/ml to plate-bound C3d by wild-type C3d (wt) compared to mutant C3d (mut1, mut2, and mut4) at several concentrations. Wt and mut1 inhibited CR2-C3d binding similarly, whereas mut2 and mut4 have lost most of their inhibitory capabilities and, thus, do not effectively interact with CR2.
Figures reprinted by permission from the AAAs: Science (2001, 292, 1725-1728) copyright 2001.
PDB entries for which this is a key reference: 1ghq.
N.Handa, E.Mizohata, S.Kishishita, M.Toyama, S.Morita, T.Uchikubo-Kamo, R.Akasaka, K.Omori, J.Kotera, T.Terada, M.Shirouzu, S.Yokoyama. (2008). Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP. J Biol Chem, 283, 19657-19664. [PubMed id: 18477562]
Figure 3.
FIGURE 3. Recognition of cAMP by the GAF-B domain of PDE10A. A, a semi-transparent surface representation, viewed from the opening of the cAMP-binding pocket. The bound cAMP molecule is represented by a yellow ball-and-stick model, with oxygen, nitrogen, and phosphorus atoms shown in red, blue, and purple, respectively. A simulated annealing omit [calc](|F[o]| - |F[c]|) map was calculated without the cAMP molecule atoms to 2.1-Å resolution, and was contoured at 3.0 . B, stereo diagram showing the cAMP recognition. The bound cAMP (yellow) and the interacting residues (white) are shown by ball-and-stick models, with oxygen, nitrogen, phosphorus, and sulfur atoms shown in red, blue, purple, and orange, respectively. Two water molecules are shown as red spheres. In the ribbon model, the β strands are cyan, the helices are salmon, the 3[10] helix is green, and the random coils are gray. Hydrogen bonds between cAMP and the protein are indicated by broken red lines.
Figure 4.
FIGURE 4. cNMP recognition by GAF domains. Hydrogen bonds are indicated by broken red lines. A, stereo diagram showing the superposition of GAF domains complexed with cNMP from PDE10A, PDE2A, and cyaB2. The GAF domains except for the helical bundles are represented by gray tube models. The cNMP molecules are represented by blue stick models. Amino acid side chains at positions equivalent to Phe^304 (PDE2A, Phe^438; cyaB2, Ile^308), Val^356 (PDE2A, Val^484; cyaB2, Ile^355), Asp^357 (PDE2A, Asp^485; cyaB2, Asp^356), Thr^360 (PDE2A, Thr^488; cyaB2, Thr^172/Asn^359), Thr^364 (PDE2A, Thr^492; cyaB2, Thr^176/Thr^363), Gln^383 (PDE2A, Glu^512; cyaB2, Gln^196/Gln^383), Val^385 (PDE2A, Val^514; cyaB2, Leu^198/Val^385), in PDE10A are shown, and backbone atoms at positions equivalent to Ile^330 (PDE2A, Ile^458; cyaB2, Ile^139/Phe^326) and Ala^331 (PDE2A, Ala^459; cyaB2, Ala^140/Ala^327) are shown. Residues making hydrophobic interactions with cNMP are orange, residues making hydrogen bonds to the O2' are sky blue, residues making water-mediated hydrogen bonds to bases are pink, and residues making hydrogen bonds to phosphate groups are green. One water molecule is shown, as a red sphere. B, stereo diagram showing the superimposed ball-and-stick models of the bases and the residues making direct hydrogen bonds to the bases. Residues in the PDE10A GAF-B domain complexed with cAMP are green, residues in the PDE2A GAF-B domain complexed with cGMP are magenta, residues in the cyaB2 GAF-A domain complexed with cAMP are yellow, and residues in the cyaB2 GAF-B domain complexed with cAMP are orange. Oxygen, nitrogen, and sulfur atoms are red, blue, and orange, respectively.
Figures reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 19657-19664) copyright 2008.
PDB entries for which this is a key reference: 2zmf.