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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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S.Tottey, K.J.Waldron, S.J.Firbank, B.Reale, C.Bessant, K.Sato, T.R.Cheek, J.Gray, M.J.Banfield, C.Dennison, N.J.Robinson. (2008). Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature, 455, 1138-1142. [PubMed id: 18948958]
Figure 3.
Figure 3: MncA and CucA have similar metal-sites. a, X-band electron paramagnetic resonance spectra of Cu^2+-CucA and Cu^2+-MncA. b, Residues (blue) surrounding the metal ions (pink) within each MncA cupin fold (amino-terminal, left panel; carboxy-terminal, right panel), with corresponding final 2F[o] - F[c] electron density maps contoured at 1.1 .
Figure 4.
Figure 4: MncA prefers Cu^2+ but entraps Mn^2+. a, Co-migration by gel-filtration of Cu^2+ (triangles) but not Mn^2+ (squares) after folding MncA (circles) in an excess of equimolar metals (left), and metals bound at increasing [Mn^2+] (right). b, Substitution of Mn^2+-MncA (filled triangles) or Mn^2+-CucA (open triangles) with Cu^2+. c, MncA metal-sites are buried with a channel to the surface only apparent in the C-terminal domain. Protein surfaces (yellow) are shown surrounding the MncA metal-sites (metals in pink, protein interior shaded grey). Chelating residues are those shown in Fig. 3. d, Signal peptides (not underlined), and twin arginines (bold). e, Regions of profiles containing MncA before (top) and after (bottom) addition of unfolded MncA to a periplasm extract. f, Bi-cupin MncA folds and entraps uncompetitive Mn^2+ in the cytoplasm, without competition from copper or Zn^2+, before Tat-export. Mono-cupin CucA (modelled) is exported unfolded via Sec and acquires competitive Cu^2+.
Figures reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 455, 1138-1142) copyright 2008.
PDB entries for which this is a key reference: 2vqa.
J.D.Mancias, J.Goldberg. (2007). The transport signal on Sec22 for packaging into COPII-coated vesicles is a conformational epitope. Mol Cell, 26, 403-414. [PubMed id: 17499046]
Figure 2.
Figure 2. Overall Structure of the Sec23/24•Sec22 Complex
(A) Ribbon diagram with Sec23 colored gray, Sec24 blue, the Sec22 longin domain red, and the Sec22 NIE segment of the SNARE motif yellow. The two views are related by a 90° rotation; on the left the membrane-proximal surface faces forward, and on the right the subtle curvature of the complex is emphasized by comparison with the surface of a 60 nm sphere (gray line).
(B) A close-up view of Sec22 in the complex, with proteins colored as in (A). Amino acid residues of the Sec22 longin domain that interact with the NIE segment of the SNARE motif are colored pink. A difference electron density (simulated-annealing omit) map for the NIE segment is drawn in green, calculated at 2.3 Å resolution and contoured at 1.6 σ. The NIE segment is drawn in yellow with oxygen atoms red and nitrogen atoms blue, and residues Asn152, Ile153, and Glu154 are labeled.
(C) Schematic diagram of Sec22 (numbering corresponds to human Sec22b). A previous analysis of S. cerevisiae Sec22 identified two elements required for efficient ER export: the longin domain, and a portion of the SNARE motif between layers −4 and −1 that includes the highly conserved NIE segment (Liu et al., 2004).
Figure 3.
Figure 3. Interaction Surfaces on Sec23/24 and Sec22
(A) The molecular surfaces of Sec23/24 and Sec22 are colored according to sequence conservation of the underlying residues in an alignment of Sec23, Sec24, and Sec22 sequences from ten organisms (see Experimental Procedures; sequence alignments for Sec24 are presented in Figures S1 and S2). Picture shows an “open book” view, with Sec22 rotated 140° from the Sec23/24 complex; for comparison, the opposite (180° rotated) surface of Sec23/24 is also shown. Protein contact regions are outlined in black, and a blue line indicates the interface of Sec23 and Sec24. Sar1 (drawn as a backbone worm in cyan) is modeled based on a previous structural analysis of the yeast Sec23/24•Sar1 complex (Bi et al., 2002).
(B) Picture shows interactions between the Sec22 longin domain (pink) and Sec24 (blue); Sec23 is colored gray, and the SNARE segment is yellow. Highly conserved residues of the α2-α3 loop of Sec22 are drawn in red; highly conserved interfacial residues of Sec24 are shown in dark blue.
Figures reprinted by permission from Cell Press: Mol Cell (2007, 26, 403-414) copyright 2007.
PDB entries for which this is a key reference: 2nup, 2nut.
G.Calero, P.Gupta, M.C.Nonato, S.Tandel, E.R.Biehl, S.L.Hofmann, J.Clardy. (2003). The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2. J Biol Chem, 278, 37957-37964. [PubMed id: 12855696]
Figure 4.
FIG. 4. Structural comparisons. a, superimposition of the residues in the binding groove of PPT1 and -2 depicted in red and cyan, respectively. The palmitate residue occupies the position observed in the crystal structure of PPT1 (for review, see "Results and Discussion"). b, superimposition between PPT1 (red) and -2 (cyan) of loop 6- 4, helix 4, and helix 5. Indicated for positional reference are the catalytic residues Ser-111 and His-283 (PPT2, steel blue) and Ser-115 and His-289 (PPT1, red).
Figure 5.
FIG. 5. Binding groove comparison. a, surface representation of PPT2 using the same orientation as in Fig. 4a to illustrate the binding groove and the lid that covers the binding groove forming a binding pocket (cyan). The area of the surface representation that corresponds to the binding pocket is semitransparent so that loop 6- 4 and helices 4 and -5 can be identified. The position of the modeled palmitate residue corresponds to the position observed in the crystal structure of PPT1. The catalytic residues Ser-111 and His-283 are indicated for reference. b, surface representation of PPT1. In contrast to PPT2 loop 6- 4 and helix 4 (red) are shifted to the left leaving the binding groove exposed to the solvent. The catalytic residues Ser-115 and His-289 as well as the palmitate residue are indicated for reference.
Figures reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 37957-37964) copyright 2003.
PDB entries for which this is a key reference: 1pja.
H.Bügl, E.B.Fauman, B.L.Staker, F.Zheng, S.R.Kushner, M.A.Saper, J.C.Bardwell, U.Jakob. (2000). RNA methylation under heat shock control. Mol Cell, 6, 349-360. [PubMed id: 10983982]
Figure 2.
Figure 2. FtsJ Has a Methyltransferase FoldStereo diagram of the FtsJ tertiary fold highlighting secondary structure elements. Secondary structures were assigned and the figure was rendered by RIBBONS ([8]). The bound AdoMet is shown in ball and stick representation.
Figure 3.
Figure 3. AdoMet Binding Interactions in FtsJ(A) Stereo diagram of the AdoMet binding site in FtsJ. In light blue are the 2σ contours of F[o]–F[c] difference map (1.7 Å native data) omitting AdoMet from the calculated structure factors. AdoMet and FtsJ contact residues are shown in ball and stick representation. Green, carbon (FtsJ); gray, carbon (AdoMet); blue, nitrogen; yellow, sulfur; red, oxygen. Figure drawn with RIBBONS.(B) Schematic diagram showing hydrogen bonds and nonpolar contacts between FtsJ and the AdoMet cofactor (green bonds). Black, carbon; blue, nitrogen; yellow, sulfur; red, oxygen; purple, nonpolar contacts. Figure drawn with LIGPLOT ([42]).
Figures reprinted by permission from Cell Press: Mol Cell (2000, 6, 349-360) copyright 2000.
PDB entries for which this is a key reference: 1eiz, 1ej0.
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