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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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K.Teilum, T.Thormann, N.R.Caterer, H.I.Poulsen, P.H.Jensen, J.Knudsen, B.B.Kragelund, F.M.Poulsen. (2005). Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles. Proteins, 59, 80-90. [PubMed id: 15690348]
Figure 5.
Figure 5. Effect of changes in G[UN] on [U] (top panel) and on m[eq,kin] ( ), m[u] ( ), and m[f] ( linear fits, and the dotted lines are 95% prediction limits for the fits.
Figure 8.
Figure 8.
Figures reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 59, 80-90) copyright 2005.
PDB entries for which this is a key reference: 1st7.
M.W.Fraaije, R.H.van den Heuvel, W.J.van Berkel, A.Mattevi. (1999). Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase. J Biol Chem, 274, 35514-35520. [PubMed id: 10585424]
Figure 1.
Fig. 1. Ribbon representation of a vanillyl-alcohol oxidase monomer. The histidyl-bound FAD cofactor is shown in a ball-and-stick model. This figure was prepared with MOLSCRIPT (55).
Figure 5.
Fig. 5. Superposition of active site residues in the unliganded H422A (shaded) and wild type VAO structures (black). This figure was prepared with MOLSCRIPT (55).
Figures reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 35514-35520) copyright 1999.
PDB entries for which this is a key reference: 1qlt, 1qlu.
T.Lührs, C.Ritter, M.Adrian, D.Riek-Loher, B.Bohrmann, H.Döbeli, D.Schubert, R.Riek. (2005). 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A, 102, 17342-17347. [PubMed id: 16293696]
Figure 2.
Fig. 2. Pairwise mutagenesis of 35LA (1-42) peptides. (A) Cartoon of intramolecular versus domain swapping-type interaction between monomers in the A (1-42) protofilament that consists of parallel, in-register -sheets exemplified by the salt bridge formed between the charged residues D23 and K28. Individual A molecules are indicated as colored bars that correspond to a cross section along the protofilament axis through the C^ atom positions of one presumed interacting pair of amino acids. The identity of each variant A peptide is indicated next to the corresponding schemes in rows 1-4. "intra" denotes the intramolecular scenario, and "inter" indicates the domain swapping-type scenario. Red diagonal crosses mark all scenarios that were considered to be incompatible with WT fibril formation. (B-J) Negative staining electron microscopy of 35LA (1-42) peptides. The variants are indicated on each image. All electron micrographs were recorded at a nominal magnification of x72,000. (Scale bar, 100 nm.
Figure 4.
Fig. 4. The 3D structure of a 35MoxA (1-42) fibril. (A and B) Ribbon diagrams of the core structure of residues 17-42 illustrating the intermolecular nature of the inter- -strand interactions. Individual molecules are colored. For example, the monomer at the odd end is shown in cyan. The -strands are indicated by arrows, nonregular secondary structure is indicated by spline curves through the C^ atom coordinates of the corresponding residues, and the bonds of side chains that constitute the core of the protofilament are shown. In B, the intermolecular salt bridge between residues D23 and K28 is indicated by dotted lines, and the two salt bridges formed by the central A (1-42) molecule are highlighted by rectangles. (C) van der Waals contact surface polarity and ribbon diagram at the odd end of the 35MoxA (1-42) protofilament comprising residues 17-42. The -sheets are indicated by cyan arrows, and nonregular secondary structure is indicated by gray spline curves. The hydrophobic, polar, negatively charged, and positively charged amino acid side chains are shown in yellow, green, red, and blue, respectively. Positively and negatively charged surface patches are shown in blue and red, respectively, and all others are shown in white. The direction of the fibril axis is indicated by an arrow pointing from even to odd. (D)(Upper) Simulation of a 35MoxA (1-42) fibril that consists of four protofilaments colored individually. Lower shows the same fibril in a noisy gray-scale image, which has been blurred corresponding to a resolution of 2 nm. In Right,a x5-magnified cross section perpendicular to the fibril axis is shown, using the same color code. Dimensions are indicated. To match the experimental twist of the protofilament of the fibril shown in E, a twist angle of 0.45° per molecule was used. (E) Two examples of cryoelectron micrographs of single 35MoxA (1-42) fibrils. (Scale bar, 50 nm.
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2005, 102, 17342-17347) copyright 2005.
PDB entries for which this is a key reference: 2beg.
J.Liu, D.W.Taylor, K.A.Taylor. (2004). A 3-D reconstruction of smooth muscle alpha-actinin by CryoEm reveals two different conformations at the actin-binding region. J Mol Biol, 338, 115-125. [PubMed id: 15050827]
Figure 4.
Figure 4. Paired and free ends aligned to R1 and R4. A and B, Paired and free ends looking approximately perpendicular to the plane of the 2-D array. C and D, Paired and free ends looking down the axis of the R1-R4 domain. In A and B the orientation of the R1-R4 domain is identical in both views and is similarly identical in C and D. Note the 90° orientation difference in the ABD in C and D.
Figure 5.
Figure 5. Models for polar and bipolar actin crosslinking. A and C, are longitudinal and axial views of the polar crosslink model produced using modified paired end conformations for the a-actinin ends. B and D, Longitudinal and axial views of the bipolar crosslink model produced using free end conformations for the a-actinin ends. The color scheme is CH1 (magenta), CH2 (red), R1-R4 (cyan) and Cam (yellow). The actin filament is green. In B and D the titin Z7 repeat is colored blue. In the polar crosslinking model, the ABD was changed from the open conformation that fit the map to a closed orientation suitable for actin binding. In addition, one ABD was reoriented so that the actin filaments could be coplanar. The a-actinin model in this case has no symmetry. In the bipolar crosslinking model, there are minimal changes from the reconstruction model and the model. The model has only near 2-fold rotational symmetry because 2-fold symmetry was not enforced for the R1-R4 domain.
Figures reprinted by permission from Elsevier: J Mol Biol (2004, 338, 115-125) copyright 2004.
PDB entries for which this is a key reference: 1sjj.