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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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J.P.Vivian, C.J.Porter, J.A.Wilce, M.C.Wilce. (2007). An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA. J Mol Biol, 370, 481-491. [PubMed id: 17521668]
Figure 3.
Figure 3. Structural differences between the RTP.C110S:nRB and RTP.C110S:sRB complexes. (a) Overlay of RTP.C110S crystal structures. The structure of the protein from the nRB complex is shown in blue and that from the sRB complex is shown in yellow. The angle between α2 and α3 is indicated for each subunit. (b) Plot of RMSD values versus residue number for each α-carbon position of the two RTP.C110S:nRB monomers (wing-up and wing-down) compared with each other (green) and with the RTP.C110S:sRB monomer structure (wing-up, red and wing-down, black). The structural superposition was calculated for all residues of each monomer, excluding 72 to 88. The greatest deviations occur at the β1-loop and wing regions. The RTP:nRB wing-down conformation is most similar to that of RTP.C110S:srB. (c) Overlay of the β1-loop structures (in stereo) of wing-down (yellow, left panel) and wing-up (yellow, right panel) monomers of RTP.C110S:nRB with RTP.C110S:sRB (grey, left panel) and apo-RTP (cyan, right panel) structures, respectively. Tyr33 is bound to DNA in the wing-down RTP.C110S:nRB and RTP.C110S:sRB structures only. (d) Overlay of the DNA structures from complexes with RTP.C110S. The nRB structure is shown in blue, the sRB in yellow. The corresponding helical axes are displayed as a continuous line and were calculated using the program CURVES.^35 (e) Plot of major and minor groove widths for each base step of the nRB DNA. The values for canonical B form DNA are shown. Figure 3. Structural differences between the RTP.C110S:nRB and RTP.C110S:sRB complexes. (a) Overlay of RTP.C110S crystal structures. The structure of the protein from the nRB complex is shown in blue and that from the sRB complex is shown in yellow. The angle between α2 and α3 is indicated for each subunit. (b) Plot of RMSD values versus residue number for each α-carbon position of the two RTP.C110S:nRB monomers (wing-up and wing-down) compared with each other (green) and with the RTP.C110S:sRB monomer structure (wing-up, red and wing-down, black). The structural superposition was calculated for all residues of each monomer, excluding 72 to 88. The greatest deviations occur at the β1-loop and wing regions. The RTP:nRB wing-down conformation is most similar to that of RTP.C110S:srB. (c) Overlay of the β1-loop structures (in stereo) of wing-down (yellow, left panel) and wing-up (yellow, right panel) monomers of RTP.C110S:nRB with RTP.C110S:sRB (grey, left panel) and apo-RTP (cyan, right panel) structures, respectively. Tyr33 is bound to DNA in the wing-down RTP.C110S:nRB and RTP.C110S:sRB structures only. (d) Overlay of the DNA structures from complexes with RTP.C110S. The nRB structure is shown in blue, the sRB in yellow. The corresponding helical axes are displayed as a continuous line and were calculated using the program CURVES.[3]^35 (e) Plot of major and minor groove widths for each base step of the nRB DNA. The values for canonical B form DNA are shown. These values were calculated with the program CURVES.[4]^35
Figure 4.
Figure 4. Summary of the protein:DNA contacts in the RTP.C110S:nRB complex. The DNA is represented as a schematic based on the output from NUCPLOT.^36 Phosphate groups are shown as circles, the sugar group as pentagons and the bases as the singe letter abbreviation of the nucleotide. Contacted components of the DNA are shown in red. The protein residues are indicated and grouped according to the structural element that they comprise in the protein. Contacts between the protein and DNA are shown as broken lines. The red broken lines indicate hydrogen bonds. Black broken lines indicate non-bonded contacts and blue broken lines are representative of water-mediated interactions. (a) Contacts between the nRB oligonucleotide and the wing-up half of the RTP.C110S dimer. (b) Contacts between the nRB oligonucleotide and the wing-down half of the RTP.C110S dimer. Figure 4. Summary of the protein:DNA contacts in the RTP.C110S:nRB complex. The DNA is represented as a schematic based on the output from NUCPLOT.[3]^36 Phosphate groups are shown as circles, the sugar group as pentagons and the bases as the singe letter abbreviation of the nucleotide. Contacted components of the DNA are shown in red. The protein residues are indicated and grouped according to the structural element that they comprise in the protein. Contacts between the protein and DNA are shown as broken lines. The red broken lines indicate hydrogen bonds. Black broken lines indicate non-bonded contacts and blue broken lines are representative of water-mediated interactions. (a) Contacts between the nRB oligonucleotide and the wing-up half of the RTP.C110S dimer. (b) Contacts between the nRB oligonucleotide and the wing-down half of the RTP.C110S dimer.
Figures reprinted by permission from Elsevier: J Mol Biol (2007, 370, 481-491) copyright 2007.
PDB entries for which this is a key reference: 2efw.
Y.Modis, S.Ogata, D.Clements, S.C.Harrison. (2003). A ligand-binding pocket in the dengue virus envelope glycoprotein. Proc Natl Acad Sci U S A, 100, 6986-6991. [PubMed id: 12759475]
Figure 2.
Fig. 2. The glycan at residue 153 in dengue 2 virus E protein. (A) The E protein dimer, viewed perpendicular to the dyad axis (and the view in Fig. 1 A). Both glycans are approximately perpendicular to the viral surface. Domain I and the attached glycan are shown in red, domain II and the attached glycan are shown in yellow, and domain III is in blue. Disulfide bridges are shown in orange. The molecule of -OG bound in the hydrophobic pocket underneath the kl hairpin is in green. A putative receptor-binding loop in domain III (residues 382-385) is marked with a triangle. (B) Enlargement of the area surrounding the glycan at residue 153 in domain I, with the structure of TBE envelope protein superimposed (gray) onto domain I of dengue virus E protein. The fusion peptide is highlighted in orange. The disulfide bridge between residues 92 and 105 is shown in green.
Figure 3.
Fig. 3. Mutations affecting the pH threshold of fusion (or virulence) in flaviviruses (36-41). The mutated residues line the interior of the ligand-binding pocket. For unconserved residues, the residue type in the virus in which the mutation was identified is listed first, followed by the residue type in dengue 2. The coloring is the same as in Fig. 1.
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (2003, 100, 6986-6991) copyright 2003.
PDB entries for which this is a key reference: 1oam, 1oan, 1oke.
PDB entries for which this is a secondary reference: 1ok8, 1uzg.
L.M.Koharudin, W.Furey, A.M.Gronenborn. (2009). A designed chimeric cyanovirin-N homolog lectin: structure and molecular basis of sucrose binding. Proteins, 77, 904-915. [PubMed id: 19639634]
Figure 1.
Figure 1. Design of LKAMG. The chimeric protein was created by combining the pseudosymmetric halves of TbCVNH and NcCVNH and possesses the CVNH fold. TbCVNH contains a single sugar binding site on domain A (magenta) and NcCVNH binds sugar only in domain B (cyan). The amino acid sequence of LKAMG comprises residues 1-39 and 90-103 of domain A of TbCVNH and residues 42-95 of domain B of NcCVNH.
Figure 3.
Figure 3. NMR and X-ray structures of LKAMG. (A) Stereo view of the 30 conformer ensemble (C representation) determined by NMR. Secondary structure elements are labeled only in (A) but apply throughout the figure. (B, C) Stereo views of the P2[1] and P2[1]2[1]2[1] X-ray models, respectively. Domain A is shown in gray throughout and domain B is colored magenta, blue, and green for the NMR ensemble, the P2[1], and the P2[1]2[1]2[1] X-ray models, respectively. (D, E, F) Comparison between the NMR and X-ray models. (D) Stereo views of the superposition between the lowest energy structure in the NMR ensemble (magenta) and the P2[1] X-ray model (blue) and (E) the P2[1]2[1]2[1] X-ray model (green). (F) Stereo views of the best-fit superposition of the two X-ray models. No significant differences are observed between the solution and crystal structures, although local details in loop conformations induced by crystal packing are present, especially for the loops that connect strands 2 and 3, strands 6 and 7, and strands 7 and 8.
Figures reprinted from Open Access publication: Proteins (2009, 77, 904-915) copyright 2009.
PDB entries for which this is a key reference: 3hnu, 3hnx, 3hp8.
J.M.Casasnovas, T.Stehle, J.H.Liu, J.H.Wang, T.A.Springer. (1998). A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1. Proc Natl Acad Sci U S A, 95, 4134-4139. [PubMed id: 9539702]
Figure 3.
Fig. 3. The dimer interface and ligand-binding residues. (A) Interacting residues in domain 1. Side chains are shown for residues that interact across the dimer interface in domain 1 (Fig. 2A). The conserved central Val-51 residue is blue, and Glu-34 is red. Salt bridges between residues at the periphery of the interface are dashed lines. (B) Stereoview (40) of the dimer. Side chains and carbons are shown for residues important in binding to LFA-1 (red and orange) (3, 37), human rhinoviruses 3, 14, 15, 36, and 41 (yellow and orange) (3-5), and P. falciparum (blue) (6). Only single amino acid substitutions that reduced binding 50% or 2 SD below control are shown.
Figure 4.
Fig. 4. A model for the ICAM-1 dimer on the cell surface. Domains 1 and 2 and their orientation in the dimer are from the crystal structure. The rod-like shape of domains 1-5 in the monomer and the bend between domains 3 and 4 are from electron microscopy (3, 36). Dimerization or proximity between domain 5 is based on hindrance of antibody binding to this domain in the dimer (25), and association at the transmembrane domain is based on its role in dimerization (24, 25).
Figures reprinted from Open Access publication: Proc Natl Acad Sci U S A (1998, 95, 4134-4139) copyright 1998.
PDB entries for which this is a key reference: 1ic1.
PDB entries for which this is a secondary reference: 1d3e, 1d3i, 1d3l.
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