ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

Gouet, Patrice

doi:10.1093/nar/gkg556

Cited by 1,276 publications

(927 citation statements)

References 20 publications

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“…The structure‐based sequence alignment was performed using Pymol (Schrodinger, 2010) and ClustalW (Thompson et al , 1994). The figure was generated using Espript (Gouet et al , 2003). …”

Section: Resultsmentioning

confidence: 99%

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

et al. 2016

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Nap1 is a histone chaperone involved in the nuclear import of H2A–H2B and nucleosome assembly. Here, we report the crystal structure of Nap1 bound to H2A–H2B together with in vitro and in vivo functional studies that elucidate the principles underlying Nap1‐mediated H2A–H2B chaperoning and nucleosome assembly. A Nap1 dimer provides an acidic binding surface and asymmetrically engages a single H2A–H2B heterodimer. Oligomerization of the Nap1–H2A–H2B complex results in burial of surfaces required for deposition of H2A–H2B into nucleosomes. Chromatin immunoprecipitation‐exonuclease (ChIP‐exo) analysis shows that Nap1 is required for H2A–H2B deposition across the genome. Mutants that interfere with Nap1 oligomerization exhibit severe nucleosome assembly defects showing that oligomerization is essential for the chaperone function. These findings establish the molecular basis for Nap1‐mediated H2A–H2B deposition and nucleosome assembly.

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“…The structure‐based sequence alignment was performed using Pymol (Schrodinger, 2010) and ClustalW (Thompson et al , 1994). The figure was generated using Espript (Gouet et al , 2003). …”

Section: Resultsmentioning

confidence: 99%

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

et al. 2016

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“…Ramachandran plot for KtrAB crystals: 0% outliers, 5.94% allowed, 94.06% preferred. Model analysis was performed with PYMOL 38 , STRAP 39 , ESPrit 40 and Hollow 41 . Complementation assay.…”

Section: Methodsmentioning

confidence: 99%

The structure of the KtrAB potassium transporter

Vieira-Pires

Szöllősi

Morais-Cabral

2013

Nature

106

163

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In bacteria, archaea, fungi and plants the Trk, Ktr and HKT ion transporters are key components of osmotic regulation, pH homeostasis and resistance to drought and high salinity. These ion transporters are functionally diverse: they can function as Na + or K + channels and possibly as cation/K + symporters. They are closely related to potassium channels both at the level of the membrane protein and at the level of the cytosolic regulatory domains. Here we describe the crystal structure of a Ktr K + transporter, the KtrAB complex from Bacillus subtilis. The structure shows the dimeric membrane protein KtrB assembled with a cytosolic octameric KtrA ring bound to ATP, an activating ligand. A comparison between the structure of KtrAB-ATP and the structures of the isolated fulllength KtrA protein with ATP or ADP reveals a ligand-dependent conformational change in the octameric ring, raising new ideas about the mechanism of activation in these transporters.The Trk/Ktr/HKT superfamily of ion transporters includes the Trk, Ktr and HKT transporter families 1 . These transporters are closely related to the superfamily of tetrameric cation channels 2-4 , which includes potassium, sodium and calcium channels. The membrane proteins in both superfamilies share the same architecture 2,5-9 : four subunits or repeats, each with the TM-P loop-TM (where TM indicates transmembrane helix) structural motif first seen in the KcsA potassium channel structure 10 , assemble to form an ion pore with a 'selectivity filter' along its central axis. In addition, the cytosolic regulatory proteins of the Trk and Ktr transporters and of the MthK 11,12 and large-conductance Ca 2+ -gated (BK) K + channels [13][14][15] are RCK (regulate conductance of K+) domains.Ktr ion transporters are crucial K + transport systems in some bacteria 16,17 , with a role in resistance to osmotic stress and high salinity by mediating the early uptake of K + (refs 16, 18). The Ktr ion transporters are composed of two essential components 3,16 : a membrane protein (KtrB or KtrD) and a cytosolic regulatory protein (KtrA or KtrC). Studies with cells show that Ktr proteins 8,19 transport K + but are also permeable to Na + , and that K + transport is ATP 20 and Na + dependent 5,8,18 . Furthermore, it has been shown that truncated KtrA forms octameric rings 21,22 and that KtrB assembles as homodimers 6,21 . The structures described here clarify the molecular basis of some of these properties as well as the structural relationship between these transporters and ion channels.

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“…We performed multiple structure-based sequence alignments manually. We prepared figures using Pymol (http://www.pymol.org) and the ESPRIPT server 39,40 .…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

Schulz

Dickmanns

Urlaub

et al. 2010

Nat Struct Mol Biol

106

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Proteins fold into their functional three-dimensional structure based on the information encoded in the residue sequence 1 . In all domains of life, various strategies evolved to assist folding processes in order to prevent immediate misfolding and aggregation of the nascent polypeptide chain. In the crowded cellular environment, protein folding is often aided by molecular chaperones. Molecular chaperones differ in size, function and energy dependence; however, all have in common to bind to the unfolded state of the protein in order to facilitate or mediate assembly of the correct three-dimensional structure 2,3 . In contrast to molecular chaperones, the intramolecular chaperones (IMCs) constitute a different class of chaperones. As part of the polypeptide chain, the IMC is typically cleaved off the target protein after the folding process is completed. Two classes of IMCs can be distinguished: class I IMCs assist the protein to fold into the correct tertiary structure, whereas class II IMCs are involved in quaternary structure assembly 4 . In contrast to many molecular chaperones, no evidence for an ATP-driven cleavage reaction could be found in IMCs. An example of a class II intramolecular chaperone has been identified in viral tailspike and fiber proteins. These proteins are functionally unrelated but share a highly conserved chaperone domain at their C terminus (C-terminal intramolecular chaperone domain, CIMCD), which is cleaved at a conserved position in an autoproteolytic reaction 5 . It was shown that the covalent linkage between the CIMCD and N-terminal pre-protein is necessary for correct folding, indicating that an in trans function of the chaperone is impossible 5 . Furthermore, it could be shown that some of the chaperone domains are exchangeable between the different preproteins 5,6 . While the three-dimensional structures of the CIMCDs are as yet unknown, the crystal structure of N-terminally truncated mature endoNF shows that the homotrimeric enzyme comprises a triple β-helix involved in substrate recognition 7 . This triple β-helix and the related triple-β-spiral motif have been identified in various proteins, which often play a role as virulence factors 8 . In triple β-helices, three polypeptide chains wind around a common threefold symmetry axis, conferring an extraordinary stability to the protein. The rigid elongated shape allows triple β-helix-comprising proteins to protrude from a pathogen's surface in order to interact with flexible host cell receptors, like lipopolysaccharides 9 . However, proper assembly of triple-β-helical folds poses to be difficult in the absence of a trimerization domain 10 . Hence, most triple β-helices depend on a C-terminal extension for trimerization and correct assembly 11 .Here we present the crystal structures of two representatives of a large group of systematically, functionally and structurally similar intramolecular chaperones: the Escherichia coli phage K1F endosilidase CIMCD and the Bacillus subtilis phage GA-1 neck appendage protein CIMCD. Furthermore...

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ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

Cited by 1,276 publications

References 20 publications

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

The structure of the KtrAB potassium transporter

Crystal structure of an intramolecular chaperone mediating triple–β-helix folding

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