PDBsum Gallery

A random selection of article figures used in PDBsum

		J.Q.Du, J.Wu, H.J.Zhang, Y.H.Zhang, B.Y.Qiu, F.Wu, Y.H.Chen, J.Y.Li, F.J.Nan, J.P.Ding, J.Li. (2008). Isoquinoline-1,3,4-trione Derivatives Inactivate Caspase-3 by Generation of Reactive Oxygen Species. J Biol Chem, 283, 30205-30215. [PubMed id: 18768468]
Figure 6. Crystal structures of caspase-3 in complexes with inhibitors. A, a ribbon diagram shows the overall structure of caspase-3. B, molecular surface maps represent the hydrophobic pocket with the bound inhibitors. C, a stereo view shows the composition of the hydrophobic pocket at the dimer interface and the oxidation of the catalytic cysteine (Cys^163) to sulfonic acid. D, the four inhibitors are superimposed at the binding site within bound compounds I, II, III, and IV colored in magenta, green, cyan, and yellow, respectively. E, a stereo view shows the catalytic active site of molecule C. The 2F[o] - F[c] sa_omit_map (1σ contour level) for the oxidized catalytic cysteine and the residues nearby are shown with cyan meshes. Figure 7. Proposed scheme for the catalytic inactivation of caspase-3 by isoquinoline-1,3,4-trione derivatives through redox cycling. In the presence of DTT in vitro and possibly dihydrolipoic acid in vivo, isoquinoline-1,3,4-trione derivatives rapidly undergo reduction to the corresponding semiquinone anion radicals (RQ^-). The reaction is reversible in the presence of atmospheric oxygen by reduction oxygen to ROS. The farther oxidation of DTT and dihydrolipoic acid intermediate also could generate ROS (38, 39). The produced ROS catalyzes the step by step oxidation of the active site cysteine of caspase-3 to the sulfonic acid. The semiquinone anion radicals may also contribute to the specific oxidation of the catalytic cysteine via a intermediate (Caspase-SH/RQ^-). Caspase-SH, caspase-SOH, caspase-SO[2]H, and caspase-SO[3]H represent the thiol, sulfenic, sulfinic, and sulfonic acid states of the catalytic cysteine.
Figures reprinted from Open Access publication: J Biol Chem (2008, 283, 30205-30215) copyright 2008.
PDB entries for which this is a key reference: 3deh, 3dei, 3dej, 3dek.
		O.Weichenrieder, K.Repanas, A.Perrakis. (2004). Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Structure, 12, 975-986. [PubMed id: 15274918]
Figure 5. Figure 5. Model for the Recognition of A-Tract DNA by L1-EN(A) Surface representation of L1-EN (colors as in Figure 2) with a docked NMR model of substrate DNA (Stefl et al., 2004) represented as ribbons. The upstream (5') and downstream (3') duplexes are lime-green and magenta, respectively. Sulfate ions on the surface of L1-EN used to position backbone phosphates of the DNA are yellow, and the scissile phosphate in the active site is cyan. Loop Bb6-Bb5 with H198 (asterisk) on its tip inserts into the wide minor groove at the TpA step. This likely bends or unwinds downstream (3') DNA, promoting the adenine to flip. Left: view as in Figure 4; Right: view as in Figure 2.(B) Model including only upstream (5') DNA and the flipped adenine downstream of the scissile bond (views and colors as in [A]).(C) APE1 bound to substrate DNA (style, views, and colors as in [A]). Surface patches corresponding to residues that have no equivalent in L1-EN and that occlude the active site cleft are in orange.
Figure reprinted by permission from Cell Press: Structure (2004, 12, 975-986) copyright 2004.
PDB entries for which this is a key reference: 1vyb.
		F.C.Peterson, B.L.Lytle, S.Sampath, D.Vinarov, E.Tyler, M.Shahan, J.L.Markley, B.F.Volkman. (2005). Solution structure of thioredoxin h1 from Arabidopsis thaliana. Protein Sci, 14, 2195-2200. [PubMed id: 15987893]
Figure 2. Figure 2. Redox-dependent structural changes in AtTrx h1. (A) HSQC spectra of oxidized (green contours) and reduced (red contours) AtTrx h1, with cross-peaks for residues with significant shift perturbations connected by arrows. (B) Combined 1H/15N shift differences are plotted as a function of AtTrx h1 sequence. (C) Ribbon diagram of AtTrx h1 NMR structure with chemical shift perturbations indicated in green (0.25-1) and magenta (>1). (D) Comparison of structures of AtTrx h1 and poplar Trx h1 (PDB code 1TI3 [PDB] ), aligned over all residues using the FATCAT servfer (Ye and Godzik 2004).
Figure reprinted by permission from the Protein Society: Protein Sci (2005, 14, 2195-2200) copyright 2005.
PDB entries for which this is a key reference: 1xfl.
		C.R.Grace, M.H.Perrin, J.Gulyas, M.R.Digruccio, J.P.Cantle, J.E.Rivier, W.W.Vale, R.Riek. (2007). Structure of the N-terminal domain of a type B1 G protein-coupled receptor in complex with a peptide ligand. Proc Natl Acad Sci U S A, 104, 4858-4863. [PubMed id: 17360332]
Figure 1. Fig. 1. 3D NMR structure of ECD1–CRF-R2 in complex with astressin. (A) Superposition of 20 energy-minimized conformers representing the 3D NMR structure of free ECD1–CRF-R2 (the backbone C^ atoms of residues 57–83 and 99–120 were superimposed). (B) Superposition of 20 energy-minimized conformers of ECD1–CRF-R2 in complex with astressin (the backbone C^ atoms of residues 57–120 of ECD1 and 30–41 of astressin were superimposed). The backbone of residues 44–122 of ECD1 is shown in magenta, and the backbone of residues Leu-27–Ile-41 of astressin is colored in green. In A and B the disulfide bonds are shown in yellow. (C) Ribbon diagram of the lowest energy conformer representing the 3D NMR structure of the ECD–CRF-R2 –astressin complex. The -sheets are shown in cyan, and the side chains of the core residues Trp-71 and Trp-109 along with the disulfide bonds are shown in yellow. The salt bridge Arg-101 (in blue)–Asp-65 (in red) is shown as dashed spine in orange. The backbone of astressin from Leu-27–Ile-41 is shown in green. (D) Side view of the ribbon diagram shown in C. MOLMOL was used to generate the figures (49). Figure 3. Fig. 3. Molecular anatomy of the residues in the interaction site between astressin and ECD1–CRF-R2 . Shown are front (A) and back (B) stereo views of the side chain interactions between the ECD1 and astressin. The backbones of astressin and ECD1 are shown as green and magenta ribbons, respectively. Hydrophobic side chains are shown in yellow, hydrogen bonds are shown in cyan, and the salt bridges Arg-35–Glu-86 and Lys-36–Glu-39 are shown in gray. All of the residues in the interaction surface are marked for clarity. "X" refers to norleucine residue (Nle).
Figures reprinted by permission from the National Academy of Sciences: Proc Natl Acad Sci U S A (2007, 104, 4858-4863) copyright 2007.
PDB entries for which this is a key reference: 2jnc, 2jnd.