SASBDB, a repository for biological small-angle scattering data

Valentini, Erica; Kikhney, Alexey; Previtali, Gianpietro; Jeffries, Cy M.; Svergun, Dmitri I.

doi:10.1093/nar/gku1047

Cited by 297 publications

(262 citation statements)

References 33 publications

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“…All individual model fits to the data were assessed using the reduced χ 2 test as well as the CorMap p value (α = 0.01), the latter being independent from correct error estimation/propagation through the data reduction process (32). The SAXS data and ab initio bead models of IcsA(53–758) have been deposited into the Small-Angle Scattering Biological Data Bank (SASBDB) (53) under the accession code SASDB95.…”

Section: Methodsmentioning

confidence: 99%

The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain

Mauricio

Jeffries

Svergun

et al. 2017

Journal of Biological Chemistry

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Shigella flexneri is a bacterial pathogen that invades cells of the gastrointestinal tract, causing severe dysentery. Shigella mediates intracellular motility and spreading via actin comet tail formation. This process is dependent on the surface-exposed, membrane-embedded virulence factor IcsA, which recruits the host actin regulator N-WASP. Although it is clear that Shigella requires N-WASP for this process, the molecular details of this interaction and the mechanism of N-WASP activation remain poorly understood. Here, we show that co-expression of full-length IcsA and the Shigella membrane protease IcsP yields highly pure IcsA passenger domain (residues 53–758). We show that IcsA is monomeric and describe the solution structure of the passenger domain obtained by small-angle X-ray scattering (SAXS) analysis. The SAXS-derived models suggest that IcsA has an elongated shape but, unlike most other autotransporter proteins, possesses a central kink revealing a distinctly curved structure. Pull-down experiments show direct binding of the IcsA passenger domain to both the WASP homology 1 (WH1) domain and the GTPase binding domain (GBD) of N-WASP and no binding to the verprolin homology/cofilin/acidic (VCA) region. Using fluorescence polarization experiments, we demonstrate that IcsA binding to the GBD region displaces the VCA peptide and that this effect is synergistically enhanced upon IcsA binding to the WH1 region. Additionally, domain mapping of the IcsA interaction interface reveals that different regions of IcsA bind to the WH1 and GBD domains of N-WASP. Taken together, our data support a model where IcsA and N-WASP form a tight complex releasing the N-WASP VCA domain to recruit the host cell machinery for actin tail formation.

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Section: Methodsmentioning

confidence: 99%

The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain

Mauricio

Jeffries

Svergun

et al. 2017

Journal of Biological Chemistry

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“…As of March 2015, BIOISIS (http://www.bioisis.net/) contained 99 structures and is supported by teams at the Advanced Light Source and Diamond, while SASBDB (http://www.sasbdb.org/) (Valentini et al, 2015) contained 195 models and 114 experimental datasets and is supported by a team at EMBL-Hamburg.…”

Section: Introductionmentioning

confidence: 99%

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

et al. 2015

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Summary Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?

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“…The final envelope was superimposed onto the crystal structure of βB2-crystallin using the program Situs (Wriggers, 2012). Experimental SAXS data and derived models of both full-length and terminally truncated βB2-crystallin have been deposited into the Small Angle Scattering Biological Data Bank (SASBDB) (Valentini et al, 2015) with the accession codes SASDBT9 and SASDBU9.…”

Section: Methodsmentioning

confidence: 99%

Human βB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study

2017

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Summary βγ-crystallins are long-lived eye lens proteins that are crucial for lens transparency and refractive power. Each βγ-crystallin comprises two homologous domains, which are connected by a short linker. γ-crystallins are monomeric, while β-crystallins crystallize as dimers and multimers. In the crystal, human βB2-crystallin is a domain-swapped dimer, while the N-terminally truncated βB1-crystallin forms a face-en-face dimer. Combining and integrating data from multi-angle light scattering, NMR and small angle X-ray scattering of full-length and terminally truncated human βB2-crystallin in solution, we show that both these βB2-crystallin proteins are dimeric, possess C2 symmetry, and are more compact than domain-swapped dimers. Importantly, no intermolecular paramagnetic relaxation enhancement effects compatible with domain-swapping were detected. Our collective experimental results unambiguously demonstrate that, in solution, human βB2-crystallin is not domain-swapped and exhibits a face-en-face dimer structure similar to the crystal structure of truncated βB1-crystallin.

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SASBDB, a repository for biological small-angle scattering data

Cited by 297 publications

References 33 publications

The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain

The Shigella Virulence Factor IcsA Relieves N-WASP Autoinhibition by Displacing the Verprolin Homology/Cofilin/Acidic (VCA) Domain

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Human βB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study

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