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PDBsum Gallery

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:
  • 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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J.W.Brown, D.Vardar-Ulu, C.J.McKnight. (2009). How to arm a supervillin: designing F-actin binding activity into supervillin headpiece. J Mol Biol, 393, 608-618. [PubMed id: 19683541]
Figure 1.
Fig. 1. The NMR solution structure of SVHP. (a) Superposition of the 22 accepted structures comprising the SVHP ensemble. (b) Ribbon diagram of the minimized average structure of SVHP aligned to (a). (c) Structural comparison of the minimized average structure of SVHP with (d) VHP (1YU5) and (e) DHP (1QZP) rotated approximately 90° to (a) and (b). The characteristic, conserved residues of the headpiece fold are drawn on each ribbon model. These include H41/Y41 (orange), the E39-K70 salt bridge (yellow), and three conserved hydrophobic residues in the C-terminal subdomain (green). The variable length loop (V-loop) of each structure is circled.
Figure 3.
Fig. 3. Electrostatic surface potential maps for SVHP, SVHP L38K, and VHP. (a) Ribbon diagram of VHP (1YU5) with key F-actin binding residues depicted and labeled, drawn in the same orientation as (b)–(d). Solvent-accessible surface maps of (b) VHP (1YU5), (c) the minimized average structure of SVHP, and (d) model of the L38K mutant of SVHP produced with Modeller 9v1^16 and colored by electrostatic potential from red (− 0.3) through white (0.0) to blue (0.3).
Figures reprinted by permission from Elsevier: J Mol Biol (2009, 393, 608-618) copyright 2009.
PDB entries for which this is a key reference: 2k6m, 2k6n.
C.Caillat, D.Topalis, L.A.Agrofoglio, S.Pochet, J.Balzarini, D.Deville-Bonne, P.Meyer. (2008). Crystal structure of poxvirus thymidylate kinase: an unexpected dimerization has implications for antiviral therapy. Proc Natl Acad Sci U S A, 105, 16900-16905. [PubMed id: 18971333]
Figure 2.
Subunit associations of vaccinia virus and human TMP kinases. (A and B) Ribbon representation of the vaccinia virus enzyme in lime green (A) and the human enzyme in pale blue (B) (PDB ID code 1e2d). The interface helices of dimers are in cyan (α2), purple (α3), and pink (α6). (C and D) Close-up of the packing between the helices in vaccinia virus (C) and human (D) enzymes at the dimer interfaces. The α3 helices are packed perpendicularly in the vaccinia enzyme (C) and antiparallel in human TMP kinase (D). His-69 closes the rear of the base binding pocket in the human enzyme and is maintained in this orientation by a hydrogen bond with Thr-106. A secondary shell made of Trp-116 and Phe-112 fills the space between helices α3 and α6 in hTMPK. Asn-65 is rotated through 120° in Vacc-TMPK compared to the human His-69 and is bound to Lys-105. Together with the lower steric hindrance of the secondary shell residues Ala-107 and Leu-111, it creates a cavity [semitransparent gray volume calculated by using CAVER (52)] between helices α3 and α6 connecting the base binding site to the protein surface.
Figure 3.
The Vacc-TMP kinase active site. (A) View of the active site with the two alternated conformations of the TDP-PPi ligands. The enzyme is rainbow colored, and TMP and PPi are shown as sticks and colored by atom type. Polar interactions are indicated by red dashes. The transferred phosphoryl group here shown at the donor site (PPi) has an alternate conformation (semitransparent phosphate) bound to the thymidine nucleotide. (B) The superimposed crystallographic structures of BVdU-MP (green sticks) and TDP (yellow sticks) at the active site of Vacc-TMPK (green). The bromovinyl group fits into a cavity (gray surface) at the rear of the base binding pocket and is specifically recognized by a halogen bond to Asn-65 (red dashes). The bromine atom is shown in its anomalous difference electron density map contoured at 5 σ. His-69, Trp-116, and Phe-112 close this cavity in the human enzyme (blue).
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2008, 105, 16900-16905) copyright 2008.
PDB entries for which this is a key reference: 2v54, 2w0s.
D.L.Lee, S.Ivaninskii, P.Burkhard, R.S.Hodges. (2003). Unique stabilizing interactions identified in the two-stranded alpha-helical coiled-coil: crystal structure of a cortexillin I/GCN4 hybrid coiled-coil peptide. Protein Sci, 12, 1395-1405. [PubMed id: 12824486]
Figure 2.
Figure 2. End-on view of the hybrid peptide analog, viewed from N- to C-terminus. Solid arrows denote predicted interchain (i to i` + 5) and intrachain (i to i + 3; i to i + 4) ion pairing between residues. Open arrows denote the hydrophobic interactions between residues a and a` or d and d`.
Figure 3.
Figure 3. Space-filling representation of the GCN4/cortexillin Hybrid 2 structure. Residues in positions a and d along the hydrophobic core are displayed in orange and green, respectively, with the exception of Asn 15 (a position) in light blue. Leu 7 (g) and Leu 26 (e) side chains are displayed in yellow. Glu 14 (g) and Lys 19' (e`) side chains are displayed in red and dark blue, with the i to i` + 5 interchain interaction shown in white.
Figures reprinted by permission from the Protein Society: Protein Sci (2003, 12, 1395-1405) copyright 2003.
PDB entries for which this is a key reference: 1p9i.
H.Attrill, A.Imamura, R.S.Sharma, M.Kiso, P.R.Crocker, D.M.van Aalten. (2006). Siglec-7 undergoes a major conformational change when complexed with the alpha(2,8)-disialylganglioside GT1b. J Biol Chem, 281, 32774-32783. [PubMed id: 16895906]
Figure 1.
FIGURE 1. Binding of the GT1b analog by Siglec-7. A, schematic representations of GT1b ganglioside (top) and the GT1b analog (bottom) are shown. Sugars not seen in the electron density are in red. B, the V-set domain of Siglec-7 was co-crystallized with a GT1b analog. For five of the seven sugar residues there was clearly defined in the electron density. A stereo image of the unbiased |F[o]| - |F[c]|, map contoured at 2.5 (gray meshwork) is shown. C, a stereo image of the glycan binding site surface. The ligand binding site is very open, and GT1b lies exposed to the solvent. The C-C' loop forms a convex shelf (marine blue), forming the base of the binding site over which the terminal of the glycan lies. The only portion of the ligand that is buried to any significant degree is the trimethylsilyl group that lies in a hydrophobic cup (green). Arg-124, the essential anchor-residue, is blue. D, the network of potential hydrogen bonds (as defined by WHATIF, Table 2) are shown as black-dashed lines. Several water molecules are stably associated with the ligand and are shown as orange spheres. E, the human CD33-related siglecs were aligned using ClustalW (58) and annotated using aln2als (courtesy of Charlie Bond, University of Dundee). The CD33-related siglecs share between 50 and 80% sequence identity in their extracellular domains. Residues showing 100% sequence conservation are shaded in black;ata lower cutoff of 75% identity the shading is gray. The secondary structure, as defined by the liganded form of Siglec-7, is depicted by arrows ( -sheets) and cylinders ( -helices) lying above the alignment. Residues of importance are highlighted by symbols lying beneath the alignment: , essential Arg; , direct interaction with glycan; , hydrophobic pocket residues which interact with the trimethylsilyl group; , position equivalent to Trp-85 in Siglec-7.
Figure 2.
FIGURE 2. Conformational comparison; GT1b with other glycans. A, in this stereo image the GT1b analog (cyan carbon atoms) from the crystal structure of Siglec-7 has been superimposed over the Gal moiety with the GD3-like glycan (black carbon atoms) from a complex with tetanus toxin (PDB code 1YYN). Despite sharing the same core residues, the ligands differ significantly, and no two residues in sequence are superimposable. Torsion angles are given in Table 3. B, superimposition of the branch point at the Gal of GT1b (shown with cyan carbons), GM1 (PDB code 3CBH, black), and GT1b (PDB code 1FV2, pink) shows that the GalNAc (1,4)Gal linkage is highly restricted due to the presence of the branch and the axial position of the Gal C4-O (labeled C4-O). The Neu5Ac (2,3)Gal branch shows some restriction in conformational freedom but to a lesser extent. Note that the Neu5Ac of GT1b is in the non-natural anomeric conformation.
Figures reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 32774-32783) copyright 2006.
PDB entries for which this is a key reference: 2hrl.
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