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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).
Note that only figures from the key and added references are displayed on the given entry's PDBsum page. Figures from the secondary references only appear on the entry's references page, which is reached via the "References" link on the left.

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Y.Miyanoiri, H.Kobayashi, T.Imai, M.Watanabe, T.Nagata, S.Uesugi, H.Okano, M.Katahira. (2003). Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics. J Biol Chem, 278, 41309-41315. [PubMed id: 12907678]
Figure 1.
FIG. 1. Gel retardation experiments as to RBD1, RBD2, and RBD1-RBD2. As shown in A, 4 fmol of 32P-labeled r(GUUAGUUAGUUAGUU) (T4-3) was incubated with 0, 1.5, 4.4, 13, 40, and 120 pmol of either RBD1 (lanes 1-6) or RBD2 (lanes 7-12). The mixtures were run on polyacrylamide gel. As shown in B, 4 fmol of 32P-labeled T4-3 was incubated with 0, 0.008, 0.04, 0.2, 1, and 5 pmol of RBD1-RBD2 and run on polyacrylamide gel (lanes 1-6).
Figure 5.
FIG. 5. The surface electrostatic potential. A, Musashi1 RBD1; B, RBD2. Positive surface potential > +5K[B]T and negative surface potential < -5K[B]T are represented in blue and red, respectively, where K[B] is the Boltzmann constant and T is the absolute temperature.
Figures reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 41309-41315) copyright 2003.
PDB entries for which this is a key reference: 1uaw.
H.Steuber, M.Zentgraf, A.Podjarny, A.Heine, G.Klebe. (2006). High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group. J Mol Biol, 356, 45-56. [PubMed id: 16337231]
Figure 6.
Figure 6. Refinement model of the ALR2 binding pocket at 0.95 Å resolution occupied by the pyridazinone inhibitor 6 shown in blue. For clarity, the specificity pocket is represented only in the open conformation. Amino acid residues are shown in orange, water molecules are indicated as red spheres. F[o] -F[c] density contoured at 3.5 s is shown in blue. It clearly depicts the positions of the inhibitor atoms.
Figure 7.
Figure 7. The F[o] -F[c] difference map next to residues in the catalytic center provides evidence for the protonation states of Tyr48, Lys77, His110, Trp111 and the pyridazinone moiety. Furthermore, a water molecule is indicated mediating a hydrogen bond network to His110 Nd2, Lys77 CO and the backbone NH groups of His46 and Val47. H bonds are shown as dotted green lines and the electron density corresponding to the hydrogen atoms is contoured in blue at 1.8 s. The inhibitor is shown in blue. The representation presents the binding pocket in two orientations: (a) the H bond interactions between the inhibitor and Tyr48 OH, His 110Ne2 and Trp111 Ne1; (b) clearly shows the threefold protonated Lys77 side-chain nitrogen atom involved in an H-bond network to Tyr48 OH, Asp43 Od2 and Cys44 CO.
Figures reprinted by permission from Elsevier: J Mol Biol (2006, 356, 45-56) copyright 2006.
PDB entries for which this is a key reference: 1z89, 1z8a.
K.C.Hsia, P.Stavropoulos, G.Blobel, A.Hoelz. (2007). Architecture of a coat for the nuclear pore membrane. Cell, 131, 1313-1326. [PubMed id: 18160040]
Figure 2.
Figure 2. Overview of the Structure of the Sec13-Nup145C Hetero-Octamer
(A) Ribbon representation of the Sec13-Nup145C hetero-octamer, showing Sec13 in yellow and orange and Nup145C in green and blue. A 90° rotated view is shown on the right. The three pseudo-two-fold axes (black ovals) that run through the hetero-octamer and the overall dimensions are indicated. The Sec13-Nup145C hetero-octamer forms a slightly bent rod.
(B) Schematic representation of the Sec13-Nup145C hetero-octamer. Magenta lines indicate interaction surfaces.
Figure 3.
Figure 3. The Interaction of the Nup145C α-Helical Domain with the Sec13 β-Propeller
(A) The ribbon representation of the Nup145C structure is shown in rainbow colors along the polypeptide chain from the N to the C terminus. The N-terminal domain invasion motif (DIM), the C-terminal α-helical domain, and their secondary structure elements are indicated.
(B) The structure of the Sec13-Nup145C heterodimer. The Nup145C^DIM (magenta), the Nup145C α-helical domain (blue), the Nup145C αB-αC connector segment (red), and the Sec13 β-propeller (yellow) are indicated; a 90° rotated view is shown on the right.
(C) Schematic representation of the Sec13-Nup145C interaction.
(D) The β-propeller domain of Sec13 in complex with the Nup145C^DIM. Sec13 is shown in yellow, and the six blades are indicated. The Nup145C^DIM forms a three-stranded seventh blade, complementing the Sec13 β-propeller domain.
(E) Schematic representation of the Sec13 β-propeller and its interaction with the Nup145C^DIM.
Figures reprinted from Open Access publication: Cell (2007, 131, 1313-1326) copyright 2007.
PDB entries for which this is a key reference: 3bg0, 3bg1.
T.L.Chapman, A.P.Heikema, A.P.West, P.J.Bjorkman. (2000). Crystal structure and ligand binding properties of the D1D2 region of the inhibitory receptor LIR-1 (ILT2). Immunity, 13, 727-736. [PubMed id: 11114384]
Figure 1.
Figure 1. LIR-1 D1D2 Crystal Structure(A) Ribbon diagram of the structure of LIR-1 D1D2. Disulfide bonds are shown in yellow, and dashed lines indicate disordered loops. Arrow indicates the location of the bond between residues 99 and 100, which can be proteolitically cleaved to generate stable fragments corresponding to D1 and D2 ([10]).(B) Topology diagram of LIR-1 D1D2. β strands are blue, 3[10] helices are green, and polyproline type II helices are red.(C) Stereoview of LIR-1 D1 (green) superimposed upon KIR2DL1 ([16]) (red). N and C termini of LIR-1 D1D2 are labeled. Cα atoms of the D1 domains of each structure were superimposed, illustrating the slight displacement of the D2 domains. Root mean square deviation (r.m.s.d) values for superpositions: 0.92 Å (71 Cα atoms) (LIR-1 D1 and KIR2DL1 D1), 1.25 Å (88 Cα atoms) (LIR-1 D2 and KIR2DL1 D2), 1.36 Å (67 Cα atoms) (LIR-1 D1 and LIR-1 D2).(D) LIR-1 D1D2 model in the region of the D1 3[10] helix superimposed on a 2.1 Å 2|F[obs]| − |F[calc]| annealed omit electron density map contoured at 1.0σ (map radius, 3.5 Å).
Figure 5.
Figure 5. Comparison of Ligand Binding Sites on LIR-1 D1D2 and KIR2DL1(A) Residues altered by site-directed mutagenesis are highlighted on a ribbon diagram of the LIR-1 D1D2 structure. Alteration of residues indicated in red resulted in changes in the affinity of LIR-1 D1D2 or LIR-2 D1D2 for UL18 (Table 2). Alteration of residues indicated in blue had no significant effect on the binding affinity.(B) Residues contributing to the KIR binding site for class I MHC molecules ([4, 42, 38, 43 and 6]) are highlighted on the structure of KIR2DL1 ( [16]).
Figures reprinted by permission from Cell Press: Immunity (2000, 13, 727-736) copyright 2000.
PDB entries for which this is a key reference: 1g0x.
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