Implementing an X-ray validation pipeline for the Protein Data Bank

Gore, Swanand; Velankar, Sameer; Kleywegt, Gerard J.

doi:10.1107/s0907444911050359

Cited by 90 publications

(95 citation statements)

References 34 publications

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“…F-actin and crenactin share the same interaction sites, despite their low sequence identity. We focus on the interfaces present in 4BQL (7) because, according to the Protein Data Bank (PDB) validation reports (18), it is of higher quality than 4CJ7 (8). The side chain and Ramachandran outliers in 4CJ7, as well as clashes in the interfaces, might distort the conclusions.…”

Section: Resultsmentioning

confidence: 99%

Archaeal actin from a hyperthermophile forms a single-stranded filament

Braun

Orlova

Valegård

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The prokaryotic origins of the actin cytoskeleton have been firmly established, but it has become clear that the bacterial actins form a wide variety of different filaments, different both from each other and from eukaryotic F-actin. We have used electron cryomicroscopy (cryo-EM) to examine the filaments formed by the protein crenactin (a crenarchaeal actin) from Pyrobaculum calidifontis, an organism that grows optimally at 90°C. Although this protein only has ∼20% sequence identity with eukaryotic actin, phylogenetic analyses have placed it much closer to eukaryotic actin than any of the bacterial homologs. It has been assumed that the crenactin filament is double-stranded, like F-actin, in part because it would be hard to imagine how a single-stranded filament would be stable at such high temperatures. We show that not only is the crenactin filament single-stranded, but that it is remarkably similar to each of the two strands in F-actin. A large insertion in the crenactin sequence would prevent the formation of an F-actin-like double-stranded filament. Further, analysis of two existing crystal structures reveals six different subunit-subunit interfaces that are filament-like, but each is different from the others in terms of significant rotations. This variability in the subunit-subunit interface, seen at atomic resolution in crystals, can explain the large variability in the crenactin filaments observed by cryo-EM and helps to explain the variability in twist that has been observed for eukaryotic actin filaments.helical polymers | variable twist | cytoskeletal filaments | crenactin A ctin is one of the most highly conserved as well as abundant eukaryotic proteins. From chickens to humans, an evolutionary separation of ∼350 million years, there are no amino acid changes in the skeletal muscle isoform of actin (1). There are at least six different mammalian isoforms that are quite similar to each other, and all seem to have diverged from a common ancestral actin gene (2). In contrast, we now know that bacteria have actin-like proteins that share a common fold (3-5) but have vanishingly little sequence similarity both among themselves and to eukaryotic actin (6).Two recent crystal structures of a crenarchaeal actin, crenactin (7, 8), raise interesting questions about the structure of the crenactin filament and its evolutionary relationship to F-actin. In both crystals (with two different space groups) crenactin forms a single-stranded filament with eight subunits per ∼420-Å righthanded turn, with a rise and rotation per subunit, therefore, of ∼53 Å and 45°, respectively. In contrast, in F-actin there is a rise and rotation of ∼55 Å and ∼27°along each of the two long-pitch right-handed strands. It was stated (9) that outside of the crystal the crenactin filaments are double-stranded, based upon the suggestion (8) that a single-stranded filament would unlikely be stable and that power spectra from crenactin filaments showed a strong layer line at ∼1/(210 Å), half of the repeat in the crystals.We have been able to ...

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Section: Resultsmentioning

confidence: 99%

Archaeal actin from a hyperthermophile forms a single-stranded filament

Braun

Orlova

Valegård

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…These structures, along with an ongoing concern for ensuring the quality of the data archive [25], motivated the wwPDB to convene an X-ray Validation Task Force (VTF) consisting of scientists with expert knowledge of crystallographic methods and validation procedures [26]. The X-ray VTF was charged with recommending best practices for validation that the wwPDB could then implement in its data-processing pipeline [27].…”

Section: Validationmentioning

confidence: 99%

“…A key component of the new system is the validation module, which embodies the recommendations of the X-ray VTF [27]. A detailed report is provided to the depositor that contains information about the quality of a structure and draws attention to any unusual features.…”

Section: Current Capabilities and Usagementioning

confidence: 99%

The Protein Data Bank archive as an open data resource

Berman

Kleywegt

Nakamura

et al. 2014

J Comput Aided Mol Des

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115

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“…compared to values at that resolution for the same amino acid or nucleotide (Gore et al, 2012;Kleywegt et al, 2004; next-to-last slider bar in Fig. 4).…”

Section: Model-to-data Matchmentioning

confidence: 99%

“…edu) and in the PHENIX crystallographic software system (Adams et al, 2010; http://phenix-online.org). Validation summaries are now available for each X-ray entry in the PDB (Protein Data Bank; Berman et al, 2000), including RNAs, at the RCSB, PDBe, and PDBj sites of the wwPDB (Berman, Henrick, & Nakamura, 2003;Gore, Velankar, & Kleywegt, 2012). Pucker diagnosis and pucker-specific target parameters aid RNA refinement in PHENIX.…”

Section: Introductionmentioning

confidence: 99%