Curated repository for small angle scattering data and models


SASBDB currently contains:


1581

experimental data sets

2457

models
455 experimental data sets on hold
476 models on hold

Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm.
SASBDB is a fully searchable curated repository of freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data.

Recent depositions:

SASDGB5 – The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide

PDZ1-2 fragment of PSD-95/Disks large homolog 4 experimental SAS data
OTHER model
Sample: PDZ1-2 fragment of PSD-95/Disks large homolog 4 monomer, 21 kDa Homo sapiens protein
Buffer: 20 mM TRIS/HCl, 150 mM NaCl + 10 mM RRESEI, pH: 8.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 11
The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand Biophysical Journal (2020)
Rodzli N, Lockhart-Cairns M, Levy C, Chipperfield J, Bird L, Baldock C, Prince S
RgGuinier 3.0 nm
Dmax 13.1 nm
VolumePorod 32 nm3

SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23)
Synthetic nanobody Sybody 23Spike glycoprotein (ACE2 receptor binding domain) experimental SAS data
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 2020 Jun 23
(2020 Jun 23)
Human serum albumin/Neprilysin fusion protein (HSA-NEP): 10 mM histidine, pH 6.5
Neprilysin - G400V mutantHuman serum albumin - C58S mutant experimental SAS data
Albumin-neprilysin fusion protein: understanding stability using small angle X-ray scattering and molecular dynamic simulations. Sci Rep 2020 Jun 22;10(1):10089
Sci Rep 10(1):10089 (2020 Jun 22)
Plasmodium falciparum lipocalin (PF3D7_0925900): Dimer-tetramer equilibrium through a concentration series (combined batch and SEC-SAXS measurements)
Plasmodium falciparum Lipocalin experimental SAS data
Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum Cell Reports 2020 Jun 31(12):107817
Cell Reports 31(12):107817 (2020 Jun)
NopAA, a type three effector from Sinorhizobium fredii USDA257 whith xyloglucanase activity
Type III effector NopAA experimental SAS data
Structural and enzymatic characterisation of the Type III effector NopAA (=GunA) from Sinorhizobium fredii USDA257 reveals a Xyloglucan hydrolase activity. Sci Rep 2020 Jun 18;10(1):9932
Sci Rep 10(1):9932 (2020 Jun 18)
DNA-binding protein HU-alpha, E34K mutant bound to 80 bp DNA (ratio DNA:Protein 1:2.5)
80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E34K experimental SAS data
Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling. Nat Commun 2020 Jun 9;11(1):2905
Nat Commun 11(1):2905 (2020 Jun 9)

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To cite SASBDB refer to: Kikhney AG, Borges CR, Molodenskiy DS, Jeffries CM, Svergun DI (2020) SASBDB: Towards an automatically curated andvalidated repository for biological scattering data. Protein Science 29(1); 66-75.