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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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S.Watanabe, T.Arai, R.Matsumi, H.Atomi, T.Imanaka, K.Miki. (2009). Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol, 394, 448-459. [PubMed id: 19769985]
Figure 4.
Fig. 4. Domain flexibility of TkHypA. (a) A stereo view of the superposition of the main chain of the two HypA molecules in the asymmetric unit. The NiBD and ZnBD of mol A are colored in green and magenta, respectively, and those of mol B are in cyan and light pink, respectively. The insertion region is omitted for clarity. (b) An anomalous difference Fourier map around the zinc finger motif of mol B contoured at 7.5σ (red).
Figure 6.
Fig. 6. Domain swapped dimer of TkHypA. (a) A stereo view of the overall structure of the TkHypA dimer shown in a ribbon representation. The NiBD, insertion region, and ZnBD of a protomer are shown in the same colors as in Fig. 1a. The corresponding regions of the counterpart are presented in a light-colored model. (b) A topology diagram of the TkHypA dimer. (c) The protomer structure in the dimer. (d) A superposition of the two dimers in the asymmetric unit based on the NiBD of the protomer.
Figures reprinted by permission from Elsevier: J Mol Biol (2009, 394, 448-459) copyright 2009.
PDB entries for which this is a key reference: 3a43, 3a44.
M.Cohen-Gonsaud, S.Ducasse, F.Hoh, D.Zerbib, G.Labesse, A.Quemard. (2002). Crystal structure of MabA from Mycobacterium tuberculosis, a reductase involved in long-chain fatty acid biosynthesis. J Mol Biol, 320, 249-261. [PubMed id: 12079383]
Figure 6.
Figure 6. Global fold and topology of the crystal structure of MabA. The secondary elements are numbered in order to highlight the similarity with the classical Rossmann fold. The figure was produced using Swiss-PdbViewer and POV-Ray™.
Figure 10.
Figure 10. Structure comparison of the active-site region of holo-KARbn and MabA. MabA is represented in green, holo-KARbn (PDB1EDO) in red, the superposition was made on the whole common core (described in the text). In the absence of cofactor, the superposition shows an important rearrangement of β5, and the rotation of the catalytic tyrosineresidue (Tyr153 in MabA and Tyr167 in KARbn). The Figure was produced using the program InsightII (MSI, USA).
Figures reprinted by permission from Elsevier: J Mol Biol (2002, 320, 249-261) copyright 2002.
PDB entries for which this is a key reference: 1uzl, 1uzm, 1uzn.
W.Meng, S.Sawasdikosol, S.J.Burakoff, M.J.Eck. (1999). Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase. Nature, 398, 84-90. [PubMed id: 10078535]
Figure 1.
Figure 1: Cbl domain structure and sequence comparisons. a, Ribbon diagram of unliganded Cbl-N. The N-terminal 4H domain is coloured yellow, the EF-hand domain green, and the SH2 domain blue. Secondary-structure elements are labelled A– D in the 4H domain and by established conventions for the EF-hand and SH2 domains. The bound Ca^2+ ion is indicated by a red sphere. Arginine 294 is universally conserved in SH2 domains and participates in phosphotyrosine coordination. b, Diagram of c-Cbl domain structure. The Cbl-N region and adjacent RING finger domain are conserved in all Cbl homologues. The C-terminal region, which contains proline-rich segments and tyrosine phosphorylation sites, is more variable and is completely absent in D-Cbl. A putative leucine zipper has been found near the C terminus of Cbl. c, Aligned sequences of the Cbl-N portion of human c-Cbl, human Cbl-b, Drosophila D-Cbl, and Sli-1. Residues that are identical in at least three of the sequences are shaded yellow. Secondary-structure elements are shown above the sequence and are coloured as in a and b. Black squares indicate residues that coordinate calcium. Red circles mark residues that interact with the bound ZAP-70 peptide. d, Structure-based sequence alignment of Cbl and Lck^23 SH2 domains. Seventy structurally equivalent residues are shaded yellow; -carbons of these seventy residues superimpose with an r.m.s.d. of 1.47 Å. The secondary-structure elements that are present in Lck and other SH2 domains, but not in the Cbl SH2 domain, are indicated by open boxes. e, Superposition of the Cbl SH2 domain (blue) with the Lck SH2 domain (yellow). The structural elements that are absent in the Cbl domain are red.
Figure 3.
Figure 3: Structure of the Cbl-N / ZAP-70 pY292 complex. a, Stereo diagram showing an -carbon trace of the complex. The bound ZAP-70 phosphopeptide is shown in magenta. b, Stereo diagram showing the interactions with the ZAP-70 phosphopeptide. The bound peptide is shown in white. Red spheres represent ordered water molecules that bridge Cbl-N and the bound peptide. Thin blue lines represent hydrogen bonds. In the phosphotyrosine pocket, Tyr 274 in Cbl makes an 'edge-face' interaction with the phosphotyrosine ring, and its hydroxyl group hydrogen-bonds to the carbonyl oxygen of Gly 291 in the ZAP-70 peptide. An arginine residue found in this position in most SH2 domains makes an 'amino–aromatic' interaction with the phosphotyrosine ring and also hydrogen-bonds with the carbonyl of the pY-1 residue of the bound peptide^8. C-terminal to the phosphotyrosine, the proline at position pY+4 in the ZAP-70 peptide binds in a hydrophobic cleft formed by Tyr 307, Phe 336 and Tyr 337, and the glutamic acid residue at pY+3 hydrogen-bonds with the backbone amide of His 320. c, Superposition of the liganded (yellow) and unliganded (blue) Cbl-N structures reveals a shift in the position of the SH2 domain upon phosphopeptide binding. The conformation of the 4H and EF-hand domains is essentially identical in the two structures. In the absence of phosphopeptide, the SH2 domain makes little contact with the 4H domain and its position is likely to vary, as we observe slightly different conformations among the three molecules in the asymmetric unit. Phosphopeptide binding induces a domain 'closure', in which the SH2 domain rotates to pack against the helical domain, completing the phosphotyrosine-binding pocket, as in d. d, Molecular surface representation of the Cbl-N domain, coloured by domain. The 4H domain (yellow) forms a portion of the phosphotyrosine-binding pocket. Residues 289–297 of the bound ZAP-70 phosphopeptide are shown as a stick model. The three N-terminal residues in the peptide are disordered and are not included. In the liganded structure, about 1, 200 Å^2 of the SH2 domain is buried as a result of interaction with the other two domains; 500 Å^2 is buried in the interface with the 4H domain, and 700 Å^2 is buried in the interface with the EF hand. The 4H and EF-hand domains share a solvent-excluding interface of 800 Å^2.
Figures reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 398, 84-90) copyright 1999.
PDB entries for which this is a key reference: 1b47, 2cbl.
M.She, C.J.Decker, D.I.Svergun, A.Round, N.Chen, D.Muhlrad, R.Parker, H.Song. (2008). Structural basis of dcp2 recognition and activation by dcp1. Mol Cell, 29, 337-349. [PubMed id: 18280239]
Figure 1.
Figure 1. Overall Structure and Structural Comparison of the Dcp1p-Dcp2n Complex
(A) Ribbon diagram of the Dcp1p-Dcp2n complex in the closed conformation cocrystallized with one ATP molecule (sticks). Dcp1p is shown in green, the N-terminal domain (NTD) of Dcp2n is shown in pink, and the C-terminal Nudix domain of Dcp2n (CTD) is shown in blue with the Nudix motif (residues 129–151) highlighted in red.
(B) Ribbon diagram of the Dcp1p-Dcp2n complex in the open conformation with the same coloring scheme and Dcp2CTD oriented as in (A).
(C) Superposition of the structures of S. pombe Dcp1p (green) and S. cerevisiae Dcp1p (purple, PDB code 1Q67). The EVH1 domain core structures are highly similar and the major differences lay in the N-terminal extension α1, except for the ScDcp1p-specific insertions (yellow).
(D) Superposition of the structures of Dcp2NTD in three conformations: open (orange), closed (blue), and free (gray, PDB code 2A6T). Helices α5 and α6 are variable among three structures.
(E) Stereo view of the superimposed structures of SpDcp2n in three conformations: open (yellow), closed (blue), and free (gray) with Dcp2CTD domains fixed in the same orientation. The Cα atoms of residues Arg95 and Ile96 in the hinge region are shown as spheres. In the closed form of Dcp2CTD, the peripheral loops in the Nudix domain that undergo conformational changes are highlighted and labeled.
Figure 6.
Figure 6. The Closed and Open Conformations of the Dcp1p-Dcp2n Complex
(A) The figure depicts the role of Dcp1p in promoting and/or stabilizing the closed form of the Dcp1p-Dcp2n complex. The side chains of residues involved in stabilizing the interaction are shown as sticks. The side-chain positions of Trp43 (cyan) are identical in the free form Dcp2p (PDB code 2A6T) and the open conformation of the Dcp1p-Dcp2n complex.
(B) Ribbon diagram of the hinge region (residues 92–96) between Dcp2NTD and Dcp2CTD in the closed Dcp1p-Dcp2n complex. Residues in the hinge region interact with both domains. The side chains of related residues are shown in sticks.
(C) In vitro decapping assay of Dcp2n WT and variants with mutations in the hinge region.
(D) In vivo decapping assay of S. cerevisiae Dcp2 WT and variants with mutations in the hinge region.
(E) Microscopic visualization of cells during mid-log phase of LSM1-GFP in dcp2Δ strains containing either wild-type (WT), vector (dcp2Δ), or dcp2 hinge region variants.
Figures reprinted from Open Access publication: Mol Cell (2008, 29, 337-349) copyright 2008.
PDB entries for which this is a key reference: 2qkl, 2qkm.