Browse by DISSEMINATION: Published

SASDPD6 – Fibronectin 2 and 3 of cell adhesion molecule L1 (L1CAM) expressed in HEK293F cells with kifunensine

Neural cell adhesion molecule L1 experimental SAS data
CORAL model
Sample: Neural cell adhesion molecule L1 monomer, 24 kDa Homo sapiens protein
Buffer: 50 mM MES pH 6.5, 150 mM NaCl, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 May 11
X‐ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1 The FASEB Journal 37(3) (2023)
Guédez G, Loers G, Jeffries C, Kozak S, Meijers R, Svergun D, Schachner M, Löw C
RgGuinier 2.9 nm
Dmax 9.6 nm
VolumePorod 72 nm3

SASDPX7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 50 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
Gordienko A, Mozhaev A, Gibizova V, Dadinova L
RgGuinier 3.8 nm
Dmax 14.0 nm
VolumePorod 32 nm3

SASDPY7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 500 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
Gordienko A, Mozhaev A, Gibizova V, Dadinova L
RgGuinier 7.4 nm
Dmax 12.0 nm

SASDPZ7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 2000 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
Gordienko A, Mozhaev A, Gibizova V, Dadinova L
RgGuinier 7.1 nm
Dmax 14.0 nm

SASDPJ3 – IMP-1 saRNA encoding NSP1-4 of VEEV and the spike glycoprotein of SARS-CoV-2

IMP-1 saRNA experimental SAS data
IMP-1 saRNA Kratky plot
Sample: IMP-1 saRNA monomer, 3720 kDa RNA
Buffer: 5 mM Sodium Citrate, pH: 6.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2021 Apr 27
Biophysical characterisation of the structure of a SARS-CoV-2 self-amplifying—RNA (saRNA) vaccine Biology Methods and Protocols (2023)
Myatt D, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock R
RgGuinier 23.8 nm
Dmax 85.9 nm
VolumePorod 6265 nm3

SASDD73 – Flavin reductase Pden_5119

NADPH-dependent FMN reductase experimental SAS data
SWISSMODEL model
Sample: NADPH-dependent FMN reductase dimer, 41 kDa Paracoccus denitrificans protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 Feb 22
Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans. Int J Mol Sci 24(4) (2023)
Kryl M, Sedláček V, Kučera I
RgGuinier 2.3 nm
Dmax 6.3 nm
VolumePorod 70 nm3

SASDKD6 – NURS complex subunit red1

NURS complex subunit red1 experimental SAS data
NURS complex subunit red1 Kratky plot
Sample: NURS complex subunit red1 monomer, 8 kDa Schizosaccharomyces pombe (strain … protein
Buffer: 20 mM HEPES, pH 7.5, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 14(1):772 (2023)
Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T
RgGuinier 2.5 nm
Dmax 8.7 nm
VolumePorod 12 nm3

SASDKE6 – Poly(A) polymerase pla1 bound to the NURS complex subunit red1

NURS complex subunit red1Poly(A) polymerase pla1 experimental SAS data
CORAL model
Sample: NURS complex subunit red1 monomer, 8 kDa Schizosaccharomyces pombe (strain … protein
Poly(A) polymerase pla1 monomer, 65 kDa Schizosaccharomyces pombe (strain … protein
Buffer: 20 mM HEPES, pH 7.5, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 14(1):772 (2023)
Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T
RgGuinier 3.3 nm
Dmax 10.7 nm
VolumePorod 138 nm3

SASDQG7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl)

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.9 nm
Dmax 20.7 nm
VolumePorod 206 nm3

SASDQH7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl) in the presence of coenzyme B12

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, 4-18 μM coenzyme B12 ligand, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.7 nm
Dmax 19.7 nm
VolumePorod 230 nm3