SASBDB entries for UniProt ID:

SASDRM2 – Chicken Netrin-1 ΔC dimer (experiment ID: sm22113-7/sample11)

UniProt ID: Q90922 (26-458) Netrin-1
Netrin-1 experimental SAS data
Sample: Netrin-1 dimer, 99 kDa Gallus gallus protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 24
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 5.8 nm
Dmax 23.0 nm
VolumePorod 142 nm3

SASDRN2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379532)

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

UniProt ID: None (None-None) Heparin oligosaccharide dp8 ammonium salt
Netrin-1Heparin oligosaccharide dp8 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp8 ammonium salt monomer, 2 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 23.5 nm
VolumePorod 729 nm3

SASDRP2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp8 (experiment ID: sm16028-7/379539)

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

UniProt ID: None (None-None) Heparin oligosaccharide dp8 ammonium salt
Netrin-1Heparin oligosaccharide dp8 ammonium salt experimental SAS data
Sample: Netrin-1 pentamer, 248 kDa Gallus gallus protein
Heparin oligosaccharide dp8 ammonium salt monomer, 2 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 6.4 nm
Dmax 21.9 nm
VolumePorod 723 nm3

SASDRQ2 – Chicken Netrin-1 ΔC bound to heparin oligosaccharide dp10 (experiment ID: sm16028-7/379533)

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 6.4 nm
Dmax 21.7 nm
VolumePorod 758 nm3

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