Browse by MODEL: Ab initio only

SASDQK6 – Monkeypox viral synthetic DNA fragment (DNA sequence 2, MP2)

Monekypox DNA sequence 1 experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 1 monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
Pereira H, Gemmill D, Siddiqui M, Vasudeva G, Patel T
RgGuinier 1.6 nm
Dmax 4.5 nm
VolumePorod 11 nm3

SASDQL6 – Monkeypox viral synthetic DNA fragment (DNA sequence 1, MP1 mutant)

Monekypox DNA sequence 1 mutant experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 1 mutant monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
Pereira H, Gemmill D, Siddiqui M, Vasudeva G, Patel T
RgGuinier 1.9 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDQM6 – Monkeypox viral synthetic DNA fragment (DNA sequence 2, MP2 mutant)

Monekypox DNA sequence 2 mutant experimental SAS data
DAMMIN model
Sample: Monekypox DNA sequence 2 mutant monomer, 6 kDa Monkeypox virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Sep 23
Mapping and characterization of G‐quadruplexes in monkeypox genomes Journal of Medical Virology 95(5) (2023)
Pereira H, Gemmill D, Siddiqui M, Vasudeva G, Patel T
RgGuinier 1.9 nm
Dmax 6.0 nm
VolumePorod 8 nm3

SASDMR5 – Tn3 family transposase (TnpA WT)

TnpA transposase experimental SAS data
GASBOR model
Sample: TnpA transposase dimer, 234 kDa Bacillus thuringiensis serovar … protein
Buffer: 50 mM HEPES, 200 mM NaCl, 100 mM L-Arg HCL, pH: 7.9
Experiment: SAXS data collected at SWING, SOLEIL on 2017 Nov 2
AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements. Nucleic Acids Res (2023)
Fernandez M, Shkumatov AV, Liu Y, Stulemeijer C, Derclaye S, Efremov RG, Hallet B, Alsteens D
RgGuinier 4.6 nm
Dmax 16.0 nm
VolumePorod 480 nm3

SASDS57 – Heterotrimeric membrane protein complex FtsB-FtsL-FtsQ

Cell division protein FtsBCell division protein FtsLCell division protein FtsQ experimental SAS data
DAMMIN model
Sample: Cell division protein FtsB hexamer, 70 kDa Escherichia coli (strain … protein
Cell division protein FtsL hexamer, 82 kDa Escherichia coli (strain … protein
Cell division protein FtsQ hexamer, 189 kDa Escherichia coli (strain … protein
Buffer: 20 mM HEPES pH 7.5, 200 mM NaCl, 0.2% of Cymal-5, pH: 7.5
Experiment: SAXS data collected at 13A, Taiwan Photon Source, NSRRC on 2022 Sep 23
Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome Nature Communications 14(1) (2023)
Nguyen H, Chen X, Parada C, Luo A, Shih O, Jeng U, Huang C, Shih Y, Ma C
RgGuinier 5.3 nm
Dmax 16.5 nm
VolumePorod 421 nm3

SASDPW6 – FF3 domain of pre-mRNA-processing factor 40 homolog A (Prp40A)

Pre-mRNA-processing factor 40 homolog A experimental SAS data
OTHER model
Sample: Pre-mRNA-processing factor 40 homolog A monomer, 9 kDa Homo sapiens protein
Buffer: 50 mM HEPES, 100 mM NaCl, 2 mM CaCl2, 1 mM TCEP, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Sep 23
Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A. Protein Sci 32(4):e4606 (2023)
Díaz Casas A, Cordoba JJ, Ferrer BJ, Balakrishnan S, Wurm JE, Pastrana-Ríos B, Chazin WJ
RgGuinier 1.6 nm
Dmax 7.2 nm
VolumePorod 13 nm3

SASDQL9 – Japanese encephalitis virus 5' TR RNA

Japanese encephaltitis 5' TR experimental SAS data
DAMMIN model
Sample: Japanese encephaltitis 5' TR monomer, 74 kDa Japanese encephalitis virus RNA
Buffer: 10 mM Bis-tris, 100 mM NaCl, 15 mM KCl 15 mM MgCl2, 10% glycerol, pH: 5
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 22
Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Res (2023)
Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR
RgGuinier 7.0 nm
Dmax 22.4 nm
VolumePorod 356 nm3

SASDQM9 – Japanese encephalitis virus 3' UTR RNA

Japanese encephalitis virus 3' UTR experimental SAS data
DAMMIN model
Sample: Japanese encephalitis virus 3' UTR monomer, 186 kDa Japanese encephalitis virus RNA
Buffer: 10 mM Bis-tris, 100 mM NaCl, 15 mM KCl 15 mM MgCl2, 10% glycerol, pH: 5
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 22
Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Res (2023)
Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR
RgGuinier 11.3 nm
Dmax 34.6 nm
VolumePorod 2900 nm3

SASDQN9 – Japanese encephalitis virus 5' TR and 3' UTR RNA complex

Japanese encephalitis virus 5' TR and 3' UTR complex experimental SAS data
MONSA model
Sample: Japanese encephalitis virus 5' TR and 3' UTR complex monomer, 260 kDa Japanese encephalitis virus RNA
Buffer: 10 mM Bis-tris, 100 mM NaCl, 15 mM KCl 15 mM MgCl2, 10% glycerol, pH: 5
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 22
Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Res (2023)
Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR
RgGuinier 12.8 nm
Dmax 40.0 nm
VolumePorod 4550 nm3

SASDPC7 – Ordered core SD1 domain of KNR4

Cell wall assembly regulator SMI1 experimental SAS data
DAMMIN model
Sample: Cell wall assembly regulator SMI1 monomer, 31 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 100 mM MES, 300 mM NaCl, pH: 6
Experiment: SAXS data collected at BM29, ESRF on 2016 Mar 18
The conserved yeast protein Knr4 involved in cell wall integrity is a multi-domain intrinsically disordered protein. J Mol Biol :168048 (2023)
Batista M, Donker EIM, Bon C, Guillien M, Caisso A, Mourey Funding L, Marie François Funding J, Maveyraud L, Zerbib D
RgGuinier 2.3 nm
Dmax 8.0 nm
VolumePorod 62 nm3