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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:
  • 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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S.Lee, A.Joshi, K.Nagashima, E.O.Freed, J.H.Hurley. (2007). Structural basis for viral late-domain binding to Alix. Nat Struct Mol Biol, 14, 194-199. [PubMed id: 17277784]
Figure 1.
Figure 1. Structure and LYPx[n]LxxL motif–binding site of the Alix V domain. (a) Overall fold of the Alix V domain. Red, helices; green, loops. (b) Location of the hydrophobic pocket with respect to the overall structure. Green, hydrophobic residues. (c) Lattice-related molecule (red) highlights the potential of this pocket for hydrophobic interactions. (d) Stick model of hydrophobic residues (green) shown under a translucent surface in the vicinity of the main hydrophobic pocket.
Figure 2.
Figure 2. Secondary structures and sequence alignment of human Alix and Alix orthologs (from Drosophila melanogaster, Caenorhabditis elegans, Dictyostelium discoideum, Arabidopsis thaliana and Saccharomyces cerevisiae). Black and yellow boxes denote strictly and highly conserved residues, respectively. Green arrowheads mark putative LYPx[n]LxxL motif–binding site residues.
Figures reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2007, 14, 194-199) copyright 2007.
PDB entries for which this is a key reference: 2ojq.
G.W.Hsu, X.Huang, N.P.Luneva, N.E.Geacintov, L.S.Beese. (2005). Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication. J Biol Chem, 280, 3764-3770. [PubMed id: 15548515]
Figure 2.
FIG. 2. [BP]dG at the post-insertion site of the BF active site. Stereoview of the structure of BF bound to BP-modified DNA duplex (red) superimposed on the structure of BF bound to unmodified DNA duplex (gray). A schematic representing the BF active site is shown below.
Figure 3.
FIG. 3. [BP]dG-induced distortions to the BF polymerase active site. A, the C:[BP]dG base pair surrounded by omit electron density contoured at 3 with hydrogen bonds represented in black (dashed lines) accompanied by lengths. B, superposition of the BP-modified DNA duplex (red) and an unmodified DNA duplex (gray). The BP moiety of the [BP]dG protrudes into the DNA minor groove. C, comparison of BF protein side chain conformations when BF is bound to C:[BP]dG (red) and C:G (gray) at the post-insertion site (n-1 position). Hydrogen bonds are represented as dashed lines. D, model of BF in a ternary complex with [BP]dG (yellow) obstructing the insertion site to an incoming dCTP. A cognate base pair is shown in gray, and hydrogen bonds are represented by dashed lines.
Figures reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 3764-3770) copyright 2005.
PDB entries for which this is a key reference: 1xc9.
R.Loris, A.Imberty, S.Beeckmans, E.Van Driessche, J.S.Read, J.Bouckaert, H.De Greve, L.Buts, L.Wyns. (2003). Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose. J Biol Chem, 278, 16297-16303. [PubMed id: 12595543]
Figure 1.
Fig. 1. Overall structure of the P. angolensis lectin. Shown is a schematic representation of the PAL dimer in two orthogonal orientations. One monomer is colored orange, the other one yellow. Manganese ions are shown as light blue spheres and calcium ions as green spheres. The bound molecules of Me- -D-glucopyranoside are shown as CPK models.
Figure 4.
Fig. 4. Binding of glucose to PAL. a, superposition of the binding sites of molecules A and B in the asymmetric unit of the Me- -D-glucose complex. b, a superposition is shown of the PAL-Me- -D-glucose (dark bonds) and the ConA-Me- -D-glucose complex (light bonds). Selected residues of PAL are labeled.
Figures reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 16297-16303) copyright 2003.
PDB entries for which this is a key reference: 1n3o, 1n3p, 1n3q.
S.G.Brohawn, T.U.Schwartz. (2009). Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice. Nat Struct Biol, 16, 1173-1177. [PubMed id: 19855394]
Figure 2.
(a) ACE1 crown-crown interaction between Nup145C and Nup84. (b) The same interaction between two Sec31 molecules (PDB 2PM6; ref. 36). The Sec31 interaction is shown without domain swapping, and the rest of the molecules are removed for clarity (see Results). Analogous juxtaposition of crown helices 6, 7 and 8 is observed in both a and b.
Figure 4.
A composite atomic model for the Y complex of the NPC, emphasizing the role of the Nup84–Nup145C edge element as a membrane curvature–stabilizing unit analogous to the Sec31–Sec31 edge element in COPII vesicle coats. The long arm of the Y complex is a composite model from crystal structures and is shown with Nup145C in blue, Sec13 in orange, Nup84 in green and Nup133 in yellow. The relative position of the N-terminal propeller of Nup133 (yellow) and the short arm components Nup120 (blue) and Nup85–Seh1 (blue–orange) are more tentatively placed and shown half-transparent (see Results for details). The long axis of the Y complex is oriented along the positively curved nuclear envelope membrane, with the concave face of the Nup84–Nup145C edge element facing the lipid bilayer. This orientation is analogous to that of the Sec31–Sec31 edge element in the COPII coat and is consistent with the evolutionary relationship between the NPC and COPII vesicle coat lattices. Notably, although the Y complex is shown facing the membrane, it is not predicted to directly contact the nuclear envelope. Rather, other nucleoporins are predicted to have roles that correspond to adaptor complexes in other vesicle coating systems that link the membrane curvature–stabilizing coat (the Y complex) to the nuclear envelope.
Figures reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 1173-1177) copyright 2009.
PDB entries for which this is a key reference: 3jro, 3jrp.