SASBDB entries for UniProt ID:

SASDRR2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379540)

UniProt ID: Q90922 (26-458) Netrin-1

UniProt ID: None (None-None) Heparin oligosaccharide dp10 ammonium salt
Netrin-1Heparin oligosaccharide dp10 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp10 ammonium salt monomer, 3 kDa Sus scrofa domesticus
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 26
The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation Nature Communications 14(1) (2023)
Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier G, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J
RgGuinier 6.5 nm
Dmax 21.9 nm
VolumePorod 769 nm3

SASDRS2 – Collagen-like peptide Mannan-binding lectin (MBL) center

UniProt ID: None (None-None) Ac-(POG)4-QG-(POG)5-NH2
Ac-(POG)4-QG-(POG)5-NH2 experimental SAS data
PYMOL model
Sample: Ac-(POG)4-QG-(POG)5-NH2 trimer, 11 kDa synthetic construct protein
Buffer: 20 mM L-histidine, 138 mM NaCl, 2.7 mM KCL,, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Feb 1
A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin. J Biol Chem 299(2):102799 (2023)
Iqbal H, Fung KW, Gor J, Bishop AC, Makhatadze GI, Brodsky B, Perkins SJ
RgGuinier 2.1 nm
Dmax 8.7 nm
VolumePorod 7 nm3

SASDRT2 – Collagen-like peptide Mannan-binding Lectin (MBL) native

UniProt ID: None (None-None) Ac-(POG)4-QG-(POG)5-NH2
Ac-(POG)4-QG-(POG)5-NH2 experimental SAS data
PYMOL model
Sample: Ac-(POG)4-QG-(POG)5-NH2 trimer, 11 kDa synthetic construct protein
Buffer: 20 mM L-histidine, 138 mM NaCl, 2.7 mM KCL,, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Feb 1
A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin. J Biol Chem 299(2):102799 (2023)
Iqbal H, Fung KW, Gor J, Bishop AC, Makhatadze GI, Brodsky B, Perkins SJ
RgGuinier 1.7 nm
Dmax 7.1 nm
VolumePorod 4 nm3

SASDR83 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 2 and 3 of SARS-CoV-2 in HEPES conditions

UniProt ID: None (None-None) Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2

UniProt ID: P0DTC9 (44-180) Nucleoprotein
Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2Nucleoprotein experimental SAS data
Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 Nucleoprotein Kratky plot
Sample: Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA
Nucleoprotein dimer, 30 kDa Severe acute respiratory … protein
Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan
RgGuinier 2.9 nm
Dmax 10.5 nm
VolumePorod 69 nm3

SASDR93 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 4 with AU extension of SARS-CoV-2 in HEPES conditions

UniProt ID: P0DTC9 (44-180) Nucleoprotein

UniProt ID: None (None-None) Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2
NucleoproteinStem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 experimental SAS data
Nucleoprotein Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 Kratky plot
Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein
Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 22 kDa Severe acute respiratory … RNA
Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan
RgGuinier 3.2 nm
Dmax 11.8 nm
VolumePorod 50 nm3

SASDRA3 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA AU extension of SARS-CoV-2 in HEPES conditions

UniProt ID: None (None-None) AU extension in the 5'-genomic end of SARS-CoV-2

UniProt ID: P0DTC9 (44-180) Nucleoprotein
AU extension in the 5'-genomic end of SARS-CoV-2Nucleoprotein experimental SAS data
AU extension in the 5'-genomic end of SARS-CoV-2 Nucleoprotein Kratky plot
Sample: AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA
Nucleoprotein dimer, 30 kDa Severe acute respiratory … protein
Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan
RgGuinier 2.6 nm
Dmax 9.0 nm
VolumePorod 46 nm3

SASDRB3 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in HEPES conditions

UniProt ID: P0DTC9 (44-180) Nucleoprotein

UniProt ID: None (None-None) Stem loop 4 in the 5'-genomic end of SARS-CoV-2
NucleoproteinStem loop 4 in the 5'-genomic end of SARS-CoV-2 experimental SAS data
Nucleoprotein Stem loop 4 in the 5'-genomic end of SARS-CoV-2 Kratky plot
Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein
Stem loop 4 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA
Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements
Karthikeyan Dhamotharan
RgGuinier 2.7 nm
Dmax 10.0 nm
VolumePorod 46 nm3

SASDRC3 – Homo-oligomeric mixture of human myelin protein zero Ig domain

UniProt ID: P25189 (30-153) Myelin protein P0
Myelin protein P0 experimental SAS data
ALPHAFOLD model
Sample: Myelin protein P0, 15 kDa Homo sapiens protein
Buffer: 50 mM NaCl, 1 mM EDTA, 20 mM TrisCl, pH: 7.6
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Jul 21
Homomeric interactions of the MPZ Ig domain and their relation to Charcot-Marie-Tooth disease Brain (2023)
Ptak C, Peterson T, Hopkins J, Ahern C, Shy M, Piper R
RgGuinier 2.9 nm
Dmax 17.0 nm

SASDRD3 – Homo-oligomeric mixture of human myelin protein zero Ig domain (W53A, R74A, D75R mutant)

UniProt ID: P25189 (30-153) Myelin protein P0 (W53A, R74A, D75R)
Myelin protein P0 (W53A, R74A, D75R) experimental SAS data
ALPHAFOLD model
Sample: Myelin protein P0 (W53A, R74A, D75R), 14 kDa Homo sapiens protein
Buffer: 50 mM NaCl, 1 mM EDTA, 20 mM TrisCl, pH: 7.6
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Jul 14
Homomeric interactions of the MPZ Ig domain and their relation to Charcot-Marie-Tooth disease Brain (2023)
Ptak C, Peterson T, Hopkins J, Ahern C, Shy M, Piper R
RgGuinier 1.9 nm
Dmax 7.0 nm

SASDRE3 – Tissue Transglutaminase + Ca: Time-resolved 0ms

UniProt ID: P21980 (1-687) Protein-glutamine gamma-glutamyltransferase 2
Protein-glutamine gamma-glutamyltransferase 2 experimental SAS data
Protein-glutamine gamma-glutamyltransferase 2 Kratky plot
Sample: Protein-glutamine gamma-glutamyltransferase 2, 77 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, 10% glycerol, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at ID7A1 BioSAXS / HP-Bio Beamline, Cornell High Energy Synchrotron Source (CHESS) on 2021 Nov 19
Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering IUCrJ 10(3):363-375 (2023)
Zielinski K, Katz A, Calvey G, Pabit S, Milano S, Aplin C, San Emeterio J, Cerione R, Pollack L
RgGuinier 4.1 nm
Dmax 16.0 nm
VolumePorod 150 nm3