SASBDB entries for UniProt ID:

SASDMJ4 – Lysozyme amyloid fibril (LAF)

UniProt ID: P00698 (19-147) lysozyme amyloid fibril
lysozyme amyloid fibril experimental SAS data
DAMMIF model
Sample: Lysozyme amyloid fibril, 14 kDa Gallus gallus protein
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 5
Effect of the concentration of protein and nanoparticles on the structure of biohybrid nanocomposites. Biopolymers 111(2):e23342 (2020)
Majorošová J, Schroer MA, Tomašovičová N, Batková M, Hu PS, Kubovčíková M, Svergun DI, Kopčanský P
RgGuinier 30.2 nm
Dmax 120.0 nm

SASDML4 – LAF + MNP (r = 5.6 nm) nanocomposite

UniProt ID: P00698 (None-None) lysozyme amyloid fibril

UniProt ID: None (None-None) Fe3O4 nanoparticles; radius 5.6 nm (AFM based)
lysozyme amyloid fibrilFe3O4 nanoparticles; radius 5.6 nm (AFM based) experimental SAS data
DAMMIF model
Sample: Lysozyme amyloid fibril, 1 kDa Gallus gallus protein
Fe3O4 nanoparticles; radius 5.6 nm (AFM based) monomer, 1 kDa
Buffer: 0.2 M glycine-HCl, 80 mM NaCl, pH: 2.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 8
Effect of the concentration of protein and nanoparticles on the structure of biohybrid nanocomposites. Biopolymers 111(2):e23342 (2020)
Majorošová J, Schroer MA, Tomašovičová N, Batková M, Hu PS, Kubovčíková M, Svergun DI, Kopčanský P
RgGuinier 29.4 nm
Dmax 80.0 nm

SASDMS4 – Listeria monocytogenes invasion protein internalin B

UniProt ID: P0DQD3 (1-320) Internalin B
Internalin B experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Internalin B monomer, 36 kDa Listeria monocytogenes serotype … protein
Buffer: 25mM Na-phosphate buffer, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2003 Nov 11
X-ray and Neutron Small-Angle Scattering Analysis of the Complex Formed by the Met Receptor and the Listeria monocytogenes Invasion Protein InlB Journal of Molecular Biology 377(2):489-500 (2008)
Niemann H, Petoukhov M, Härtlein M, Moulin M, Gherardi E, Timmins P, Heinz D, Svergun D
RgGuinier 2.8 nm
Dmax 9.6 nm
VolumePorod 54 nm3

SASDMT4 – Complex of Met receptor with InlB

UniProt ID: P16056 (25-927) Hepatocyte growth factor receptor

UniProt ID: P0DQD3 (1-320) Internalin B
Hepatocyte growth factor receptorInternalin B experimental SAS data
SASREF CV model
Sample: Hepatocyte growth factor receptor monomer, 100 kDa Mus musculus protein
Internalin B monomer, 36 kDa Listeria monocytogenes serotype … protein
Buffer: 25mM Na-phosphate buffer, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2004 Mar 1
X-ray and Neutron Small-Angle Scattering Analysis of the Complex Formed by the Met Receptor and the Listeria monocytogenes Invasion Protein InlB Journal of Molecular Biology 377(2):489-500 (2008)
Niemann H, Petoukhov M, Härtlein M, Moulin M, Gherardi E, Timmins P, Heinz D, Svergun D
RgGuinier 4.6 nm
Dmax 16.0 nm
VolumePorod 270 nm3

SASDMU4 – Retinoic acid receptor RXR-alpha ligand binding domain (LBD)

UniProt ID: P19793 (231-458) Retinoic acid receptor RXR-alpha
Retinoic acid receptor RXR-alpha experimental SAS data
CUSTOM IN-HOUSE model
Sample: Retinoic acid receptor RXR-alpha dimer, 51 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, 100 mM KCl, 5% glycerol, 2 mM Chaps, and 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Oct 7
Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein Biochemistry 55(12):1741-1748 (2016)
Belorusova A, Osz J, Petoukhov M, Peluso-Iltis C, Kieffer B, Svergun D, Rochel N
RgGuinier 2.5 nm
Dmax 8.3 nm
VolumePorod 60 nm3

SASDMV4 – Full-length Retinoic acid receptor RXR-alpha in complex with Ramp2 DNA

UniProt ID: P19793 (1-462) Retinoic acid receptor RXR-alpha

UniProt ID: None (None-None) Ramp2 DNA
Retinoic acid receptor RXR-alphaRamp2 DNA experimental SAS data
EOM/RANCH model
Sample: Retinoic acid receptor RXR-alpha dimer, 102 kDa Homo sapiens protein
Ramp2 DNA monomer, 11 kDa DNA
Buffer: 20 mM Tris, 50 mM NaCl, 50 mM KCl, 5% glycerol, 2 mM Chaps, and 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 May 7
Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein Biochemistry 55(12):1741-1748 (2016)
Belorusova A, Osz J, Petoukhov M, Peluso-Iltis C, Kieffer B, Svergun D, Rochel N
RgGuinier 4.4 nm
Dmax 13.9 nm
VolumePorod 161 nm3

SASDMW4 – Retinoic acid receptor RXR-alpha N-terminal and DNA binding domains (DBD) in complex with Ramp2 DNA

UniProt ID: None (None-None) Ramp2 DNA

UniProt ID: P19793 (1-206) Retinoic acid receptor RXR-alpha
Ramp2 DNARetinoic acid receptor RXR-alpha experimental SAS data
EOM/RANCH model
Sample: Ramp2 DNA monomer, 11 kDa DNA
Retinoic acid receptor RXR-alpha dimer, 44 kDa Homo sapiens protein
Buffer: 20 mM Tris, 50 mM NaCl, 50 mM KCl, 5% glycerol, 2 mM Chaps, and 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Jul 17
Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein Biochemistry 55(12):1741-1748 (2016)
Belorusova A, Osz J, Petoukhov M, Peluso-Iltis C, Kieffer B, Svergun D, Rochel N
RgGuinier 4.3 nm
Dmax 14.3 nm
VolumePorod 89 nm3

SASDMX4 – Retinoic acid receptor RXR-alpha DNA binding (DBD) and ligand binding (LBD) domains in complex with Ramp2 DNA

UniProt ID: None (None-None) Ramp2 DNA

UniProt ID: P19793 (None-None) Retinoic acid receptor RXR-alpha
Ramp2 DNARetinoic acid receptor RXR-alpha experimental SAS data
CORAL model
Sample: Ramp2 DNA monomer, 11 kDa DNA
Retinoic acid receptor RXR-alpha dimer, 74 kDa Homo sapiens protein
Buffer: 20 mM Tris, 50 mM NaCl, 50 mM KCl, 5% glycerol, 2 mM Chaps, and 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Oct 7
Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein Biochemistry 55(12):1741-1748 (2016)
Belorusova A, Osz J, Petoukhov M, Peluso-Iltis C, Kieffer B, Svergun D, Rochel N
RgGuinier 3.6 nm
Dmax 12.2 nm

SASDMY4 – Retinoic acid receptor RXR-alpha DNA binding domain (DBD) in complex with Ramp2

UniProt ID: None (None-None) Ramp2 DNA

UniProt ID: P19793 (None-None) Retinoic acid receptor RXR-alpha
Ramp2 DNARetinoic acid receptor RXR-alpha experimental SAS data
CUSTOM IN-HOUSE model
Sample: Ramp2 DNA monomer, 11 kDa DNA
Retinoic acid receptor RXR-alpha dimer, 20 kDa Homo sapiens protein
Buffer: 20 mM Tris, 50 mM NaCl, 50 mM KCl, 5% glycerol, 2 mM Chaps, and 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Oct 7
Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein Biochemistry 55(12):1741-1748 (2016)
Belorusova A, Osz J, Petoukhov M, Peluso-Iltis C, Kieffer B, Svergun D, Rochel N
RgGuinier 1.9 nm
Dmax 5.8 nm

SASDMZ4 – Mixture of estrogen-related receptor gamma:Inverse repeat IR3 DNA - 6:3 and 2:1 complexes - at 2.9 mg/ml

UniProt ID: P62508 (122-458) Estrogen-related receptor gamma

UniProt ID: None (None-None) Inverse repeat IR3 DNA
Estrogen-related receptor gammaInverse repeat IR3 DNA experimental SAS data
SASREF MX model
Sample: Estrogen-related receptor gamma hexamer, 230 kDa Homo sapiens protein
Inverse repeat IR3 DNA trimer, 46 kDa DNA
Buffer: 20 mM Tris-HCl, 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 1% (v/v) glycerol, and 1 mM CHAPS, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Mar 3
Reconstruction of Quaternary Structure from X-ray Scattering by Equilibrium Mixtures of Biological Macromolecules Biochemistry 52(39):6844-6855 (2013)
Petoukhov M, Billas I, Takacs M, Graewert M, Moras D, Svergun D
RgGuinier 4.7 nm
Dmax 14.6 nm