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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:
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S.Birtalan, P.Ghosh. (2001). Structure of the Yersinia type III secretory system chaperone SycE. Nat Struct Biol, 8, 974-978. [PubMed id: 11685245]
Figure 1.
Figure 1. Structure of SycE. a, Ribbon diagram (monomer A in blue and monomer B in red). b, C trace in stereo view. c, Topology representation ( -helices as rectangles and -strands as arrows) with loops 4 and 5 labeled. (a,b) and Figs 2a,b, 4c were created with MOLSCRIPT28 and RASTER3D^29.
Figure 4.
Figure 4. Potential interaction sites. a, Electrostatic potential mapped onto the molecular surface of the SycE dimer. Red is negative (-10 kT), and blue is positive (+10 kT). The blue patch in the middle is formed by Lys 75 and Arg 92. b, Two large hydrophobic patches are located on the molecular surface of SycE dimer. Surfaces corresponding to hydrophobic side chains are colored green. c, SycE dimer in C trace with side chains that form the most electronegative area in red bonds and surface-exposed hydrophobic patches in green bonds. The electronegative area is formed by Asp 55, Asp 58, Glu 59, Glu 61, Asp 81, Glu 82 and Glu 115. Hydrophobic patch 1 is formed by residues Phe 49, Ile 68, Phe 69, Val 88 and Trp 90,and patch 2 by residues Phe 12, Leu 15, Leu 17, Ile 27, Val 29, Val 31, Phe 34, Tyr 104, Leu 107 and Val 111. d, Sequence of the minimal SycE-binding domain of YopE (residues 15 -50) and a second potential binding site (residues 51 -77), with residues conserved or conservatively substituted in ExoS highlighted in blue. (a,b) were made with GRASP31.
Figures reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 974-978) copyright 2001.
PDB entries for which this is a key reference: 1jya.
PDB entries for which this is a secondary reference: 1md1, 1n5b.
C.Chen, R.Brock, F.Luh, P.J.Chou, J.W.Larrick, R.F.Huang, T.H.Huang. (1995). The solution structure of the active domain of CAP18--a lipopolysaccharide binding protein from rabbit leukocytes. FEBS Lett, 370, 46-52. [PubMed id: 7649303]
Figure 2.
Fig. 2. Representative 13 TOCSY NMR pectrum of the 'fingerprint' region at 80 ms mixing time, showing the long range connectivties. Sample contains 2 mM CAPl8106-137 in ]0 mM phosphate uffer, pH 3.5, in 20/D2OFEFE = 60:10:30 (v/v/v) solvent at 3 ! 5K. The assign- ments are also given on the spectrum.
Figure 4.
Fig. 4. (a) Superimposition of fifteen backbone structures of CAPI 8~0~-t37 deduced from 263 nOe constraints and refined with simulated annealing protocol in XPLOR program. The fifteen structures have the lowest overall energies and contain no single nOe violation greater than 0.3/~,. (b) Helical wheel plot of CAPI 8~0t37 showing the clustering f positively charged groups and the hydrophobic groups.
Figures reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (1995, 370, 46-52) copyright 1995.
PDB entries for which this is a key reference: 1lyp.
D.H.Anderson, M.R.Sawaya, D.Cascio, W.Ernst, R.Modlin, A.Krensky, D.Eisenberg. (2003). Granulysin crystal structure and a structure-derived lytic mechanism. J Mol Biol, 325, 355-365. [PubMed id: 12488100]
Figure 1.
Figure 1. Ribbon representation of the granulysin five-helix bundle. (a) Numbers label helices 1 through 5, and N and C denote N and C termini. Molscript[54.] automatically assigned the backbone geometry as helix (cyan) or coil (white). Molscript interprets the borderline geometry between helices 3 and 4 as a bent helix. The same transition was depicted as coil when the data resolution was 1.5 Å. The two disulfide bonds and the solvent ions (sulfate and N-morpholino propanesulfonate) are shown as ball-and-stick figures (white carbon, blue nitrogen, red oxygen, green sulfur atoms). Coordination of negative solvent ions in the region at the top of this Figure could indicate the orientation of initial approach to the bacterial membrane. The membrane would run left to right across the top of this Figure (in an x-z plane; see Figure 3). The crystal y direction (indicated at lower right) is slightly tilted from vertical to clarify representation of the voids. (b) Ribbon representation of granulysin seen from the left of (a) (crystal directions are shown at lower left). Disulfide bonds connect helices 1 and 5 (at left) and 2 and 3 (at right). Hydrophobic side-chains loosely fill the core volume, leaving enclosed voids represented by wire frame. The enclosed volumes identified by VOIDOO (see Materials and Methods) are 14 Å3 (blue), 10.6 Å3 (green), and 5 Å3 (magenta). Unenclosed caves are omitted from this Figure. In the text, we propose that the loose core packing facilitates scissors motion: The left and right helix pairs move out of and into the paper, hinged by backbone torsions in the coil regions at the bottom of this Figure. Preliminary ionic membrane contact drives scissors exposure of hydrophobic surface of the most membrane-lytic portion of the molecule (Helix 3). This Figure was produced with Molscript,[54.] VOIDOO, [51.] XtalView, [55.] Raster3D, [56.] and PhotoShop (Adobe).
Figure 2.
Figure 2. Contacts of sulfate ions. The sulfate hydrogen bonds and salt bridges (combination ionic and hydrogen bond interactions) listed in Table 2 are shown here in a stereo pair. The viewpoint is above Figure 1; crystal axis orientations are the same as in Figure 3. The central granulysin molecule is summarized as light gray ribbons (Helix 3 is labeled H3; termini are labeled N and C). Selected side-chains (identified by one-letter residue codes) and solvent species (for example, 81 means sulfate 81) are shown as ball-and-stick figures. Oxygen atoms are red, nitrogen atoms are blue, and sulfur atoms are green. Carbon atoms of the central molecule are light gray. Symmetry-related granulysin atoms are shown with C atoms colored orange for the same x-z layer, and yellow for the next x-z layer up in the y direction (up refers to Figure 1 and Figure 5). Arg51 at left (R51; orange) is related to Arg51 at right by an x,y,z -1 operation. Arg38 at right (R38; orange) is related to Arg38 at left by an x,y,z+1 operation. The side-chains with yellow atoms are related to the central molecule by a 1 -x,y+1/2,1 -z operation, except Lys15 (K15 at bottom) by -x,y+1/2,1 -z. The location of Trp41 (W41, left of center) indicates the membrane-lytic surface of Helix 3. Both conformations are shown for each discretely disordered side-chain interacting with a sulfate. Sulfate hydrogen bonds and salt bridges are shown as green dotted lines. Some of the electric field interactions are shown by adjacency (see Table 2).
Figures reprinted by permission from Elsevier: J Mol Biol (2003, 325, 355-365) copyright 2003.
PDB entries for which this is a key reference: 1l9l.
R.V.Stahelin, D.Karathanassis, K.S.Bruzik, M.D.Waterfield, J.Bravo, R.L.Williams, W.Cho. (2006). Structural and membrane binding analysis of the Phox homology domain of phosphoinositide 3-kinase-C2alpha. J Biol Chem, 281, 39396-39406. [PubMed id: 17038310]
Figure 1.
FIGURE 1. PI3K-C2 PX domain overall structure. A, ribbon diagram of the overall fold of the PI3K-C2 PX domain colored from blue at the N terminus to red at the C terminus. B, superposition of the C trace of the PI3K-C2 PX domain (red) on the p40^phox PX domain (green). The disordered PP[II]/ 2 loop in the PI3K-C2 PX domain is represented by the dashed line. Molecular illustrations were prepared using the program PyMOL.
Figure 9.
FIGURE 9. Monolayer penetration analysis of PI3K-C2 and its isolated domains. A, was measured as a function of [0] for the PI3K-C2 C2 domain with POPC/POPE (80:20) (•), POPC/POPE/PtdIns(4,5)P[2] (78:20:2) ( ), and POPC/POPE/PtdIns(3,4)P[2] (78:20:2) ( ), and POPC/POPE/PtdIns(3,4,5)P[3] (78:20:2) ( ) monolayers. PI3K-C2 PX domain ( ) is also shown as a control. B, was measured as a function of [0] using a POPC/POPE/PtdIns(4,5)P[2] (78:20:2) monolayer for the full-length PI3K-C2 (•), R1503A ( ), and PI3K-C2 PX domain ( ). The penetration of the full-length PI3K-C2 into a POPC/POPE (80:20) monolayer is also shown as a control ( ). The subphase was 10 mM HEPES buffer, pH 7.4, containing 0.16 M KCl for all experiments. Data represent the average of duplicate measurements.
Figures reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 39396-39406) copyright 2006.
PDB entries for which this is a key reference: 2iwl.
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