Fast native-SAD phasing for routine macromolecular structure determination

Weinert, T.; Oliéric, V.; Waltersperger, S.; Panepucci, Ezequiel; Chen, Lirong; Zhang, Hua; Zhou, Da‐Yong; Rose, John P.; Ebihara, Akio; Kuramitsu, Seiki; Li, Dianfan; Howe, Nicole; Schnapp, Gisela; Pautsch, Alexander; Bargsten, Katja; Prota, A.E.; Surana, Parag; Kottur, J.; Nair, D.T.; Basilico, Federica; Cecatiello, Valentina; Pasqualato, Sebastiano; Boland, Andreas; Weichenrieder, Oliver; Wang, Bi Cheng; Steinmetz, Michel O.; Caffrey, Martin; Wang, Meitian

doi:10.1038/nmeth.3211

Cited by 117 publications

(149 citation statements)

References 32 publications

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“…On a single crystal, 4 × 360° data sets were collected at 100 K at a wavelength of 2.075 Å with 0.1° oscillation 0.1 s exposure in four different orientations of a multi‐axis goniometer (Waltersperger et al , 2015), as previously described (Weinert et al , 2015). The sample‐to‐detector distance was set to 120 mm.…”

Section: Methodsmentioning

confidence: 99%

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

et al. 2017

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The superfamily 1B (SF1B) helicase Sen1 is an essential protein that plays a key role in the termination of non‐coding transcription in yeast. Here, we identified the ~90 kDa helicase core of Saccharomyces cerevisiae Sen1 as sufficient for transcription termination in vitro and determined the corresponding structure at 1.8 Å resolution. In addition to the catalytic and auxiliary subdomains characteristic of the SF1B family, Sen1 has a distinct and evolutionarily conserved structural feature that “braces” the helicase core. Comparative structural analyses indicate that the “brace” is essential in shaping a favorable conformation for RNA binding and unwinding. We also show that subdomain 1C (the “prong”) is an essential element for 5′‐3′ unwinding and for Sen1‐mediated transcription termination in vitro. Finally, yeast Sen1 mutant proteins mimicking the disease forms of the human orthologue, senataxin, show lower capacity of RNA unwinding and impairment of transcription termination in vitro. The combined biochemical and structural data thus provide a molecular model for the specificity of Sen1 in transcription termination and more generally for the unwinding mechanism of 5′‐3′ helicases.

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Section: Methodsmentioning

confidence: 99%

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

et al. 2017

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“…3b) and, if necessary, modify the parameters of the proposed strategy. For experiments aimed at de novo structure solution, the collection of highly redundant data is often advisable, and this becomes even more relevant when weak anomalous signals are to be exploited (Dauter & Adamiak, 2001;Cianci et al, 2008;Akey et al, 2014;Weinert et al, 2015;Liu & Hendrickson, 2015).…”

Section: Calculation Of Data-collection Strategiesmentioning

confidence: 99%

“…Nevertheless, in experiments where anomalous signals are small (i.e. S-SAD; Hendrickson & Teeter, 1981;Dauter et al, 1999;Liu & Hendrickson, 2015;Weinert et al, 2015) care must be taken to reduce systematic errors and, most of all, errors introduced by radiation damage. Radiation damage is exacerbated in MAD/SAD experiments because it not only results in a decrease, as a function of absorbed X-ray dose (Seltzer, 1993;Holton, 2009), in the resolution to which a crystal diffracts, it also causes specific chemical damage including disulfide-bond breakage (Weik et al, 2000;Leiros et al, 2001;Ennifar et al, 2002), changes in electronic state (Berglund et al, 2002;Schlichting et al, 2000) and, very importantly, reduction in the 'occupancy' of anomalous scatterers (Ramagopal et al, 2005;Evans et al, 2003;Ravelli et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Facilitating best practices in collecting anomalous scattering data forde novostructure solution at the ESRF Structural Biology Beamlines

Sanctis¹,

Oscarsson²,

Попов³

et al. 2016

Acta Cryst Sect D Struct Biol

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The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic dataprocessing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated.

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“…Experimental advances at synchrotron beamlines allowing to collect more precise data through highly redundant datasets (Dauter and Adamiak, 2001;Broennimann et al, 2006), maximize the anomalous signal at longer wavelengths (Yang et al, 2003;Weinert et al, 2015), low-noise X-ray detectors (Mueller, Wang and Schulze-Briese, 2012) and improvement in the computing programs are pushing a revival of native phasing, this time on much more complex structures than those of crambin or lysozyme. Indeed, structures as large as 1148 independent amino acids have been phased at 2.8 Å from the inherent sulfur in the protein (Liu et al, 2012).…”

Section: Experimental Phasing With Inherent Anomalous Signal: Native mentioning

confidence: 99%

Crystallographic structure solution

Millán¹,

Usón²

2015

Arbor

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The three-dimensional view of molecules at the atomic level provided by X-ray crystallography is not only extremely informative but is also easily and intuitively understood by humans, who very much rely on their vision. However, unlike microscopy, this technique does not directly yield an image. The structural model cannot be directly calculated from the diffraction data, as only the intensities of scattered beams and not their phases are experimentally accessible. In order to obtain the 3-dimensional structure phases have to be obtained by either additional experimental or computational methods. This is known as the phase problem in crystallography. In this manuscript we provide an overview of major milestones along the quest for the lost phases.KEYWORDS: phase problem; constraints; structure factors; Fourier maps; search; minimization; maximum-likelihood; optimization; restraints; X-rays. RESUMEN: La cristalografía proporciona una visión tridimensional de las moléculas a un nivel de detalle atómico, que no sólo resulta muy informativa sino que además puede ser fácil e intuitivamente comprendida por seres tan predominantemente visuales como solemos ser los humanos. Sin embargo, al contrario que la microscopía, esta técnica no ofrece directamente una imagen y el modelo estructural no puede calcularse directamente a partir de los datos de difracción, ya que solamente las intensidades de los rayos difractados y no sus fases son accesibles a la medida experimental. Para determinar la estructura tridimensional las fases deben ser obtenidas por medio de métodos adicionales, bien experimentales o computacionales. Esto constituye el problema de la fase en cristalografía. En este artículo ofreceremos una visión general de los principales hitos en la búsqueda de las fases perdidas.PALABRAS CLAVE: problema de la fase; constricciones; factores de estructura; mapas de Fourier; métodos de búsqueda; minimización; máxima verosimilitud; optimización; restricciones; rayos-X.

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Fast native-SAD phasing for routine macromolecular structure determination

Cited by 117 publications

References 32 publications

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

Sen1 has unique structural features grafted on the architecture of the Upf1‐like helicase family

Facilitating best practices in collecting anomalous scattering data forde novostructure solution at the ESRF Structural Biology Beamlines

Crystallographic structure solution

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