Browse by MODEL: Ab initio only

SASDGF6 – G-quadruplex DNA from Hepatitis B virus (mutant)

G-quadruplex mutant experimental SAS data
DAMFILT model
Sample: G-quadruplex mutant monomer, 6 kDa Hepatitis B virus DNA
Buffer: 20 mM HEPES, 100 mM KCl, 1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Jan 15
G-quadruplex from HBV genome
Trushar Patel
RgGuinier 1.7 nm
Dmax 5.5 nm
VolumePorod 11 nm3

SASDSJ5 – 15mer poly-ADP ribose (PAR15) in 100mM NaCl

15mer of adenosine diphosphate ribose (poly-ADP ribose) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: 15mer of adenosine diphosphate ribose (poly-ADP ribose) monomer, 8 kDa synthetic construct
Buffer: 100 mM NaCl, 20 mM Tris-HCl, pH: 7.4
Experiment: SAXS data collected at ID7A1 BioSAXS / HP-Bio Beamline, Cornell High Energy Synchrotron Source (CHESS) on 2022 Apr 21
Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 15(1):7901 (2024)
Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL
RgGuinier 2.4 nm
Dmax 10.0 nm
VolumePorod 15 nm3

SASDSK5 – 15mer poly-ADP ribose (PAR15) in 100mM NaCl + 1mM MgCl2

15mer of adenosine diphosphate ribose (poly-ADP ribose) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: 15mer of adenosine diphosphate ribose (poly-ADP ribose) monomer, 8 kDa synthetic construct
Buffer: 20 mM Tris-HCl, 1 mM MgCl2, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at ID7A1 BioSAXS / HP-Bio Beamline, Cornell High Energy Synchrotron Source (CHESS) on 2022 Apr 21
Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 15(1):7901 (2024)
Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL
RgGuinier 2.3 nm
Dmax 9.0 nm
VolumePorod 14 nm3

SASDSL5 – 22mer poly-ADP ribose (PAR22) in 100mM NaCl

22mer of adenosine diphosphate ribose (poly-ADP ribose) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: 22mer of adenosine diphosphate ribose (poly-ADP ribose) monomer, 12 kDa synthetic construct
Buffer: 100 mM NaCl, 20 mM Tris-HCl, pH: 7.4
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2022 Apr 21
Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 15(1):7901 (2024)
Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL
RgGuinier 3.3 nm
Dmax 14.0 nm
VolumePorod 32 nm3

SASDSM5 – 22mer poly-ADP ribose (PAR22) in 100mM NaCl + 1mM MgCl2

22mer of adenosine diphosphate ribose (poly-ADP ribose) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: 22mer of adenosine diphosphate ribose (poly-ADP ribose) monomer, 12 kDa synthetic construct
Buffer: 20 mM Tris-HCl, 1 mM MgCl2, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2022 Apr 21
Cation-induced intramolecular coil-to-globule transition in poly(ADP-ribose). Nat Commun 15(1):7901 (2024)
Wang T, Coshic K, Badiee M, McDonald MR, Aksimentiev A, Pollack L, Leung AKL
RgGuinier 2.6 nm
Dmax 10.5 nm
VolumePorod 21 nm3

SASDS67 – Complex of BCL-6 corepressor linker-PUFD bound to Polycomb group RING finger protein 1 RAWUL, Lysine-specific demethylase 2B F-box-LRRs, and S-phase kinase-associated protein 1

BCL-6 corepressorLysine-specific demethylase 2BPolycomb group RING finger protein 1S-phase kinase-associated protein 1 experimental SAS data
OTHER model
Sample: BCL-6 corepressor monomer, 16 kDa Homo sapiens protein
Lysine-specific demethylase 2B monomer, 32 kDa Homo sapiens protein
Polycomb group RING finger protein 1 monomer, 13 kDa Homo sapiens protein
S-phase kinase-associated protein 1 monomer, 19 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2022 Sep 1
Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation. Commun Biol 7(1):1112 (2024)
Chen R, Shen F, Zhang Y, Sun M, Dong Y, Yin Y, Su C, Peng C, Liu J, Xu J
RgGuinier 3.3 nm
Dmax 11.5 nm
VolumePorod 118 nm3

SASDS77 – Complex of BCL-6 corepressor ANK-linker-PUFD bound to Polycomb group RING finger protein 1 RAWUL, Lysine-specific demethylase 2B F-box-LRRs, and S-phase kinase-associated protein 1

Lysine-specific demethylase 2BPolycomb group RING finger protein 1S-phase kinase-associated protein 1BCL-6 corepressor experimental SAS data
OTHER model
Sample: Lysine-specific demethylase 2B monomer, 32 kDa Homo sapiens protein
Polycomb group RING finger protein 1 monomer, 13 kDa Homo sapiens protein
S-phase kinase-associated protein 1 monomer, 19 kDa Homo sapiens protein
BCL-6 corepressor monomer, 32 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2021 Jul 16
Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation. Commun Biol 7(1):1112 (2024)
Chen R, Shen F, Zhang Y, Sun M, Dong Y, Yin Y, Su C, Peng C, Liu J, Xu J
RgGuinier 3.9 nm
Dmax 16.5 nm
VolumePorod 190 nm3

SASDVE2 – Human Haemoglobin (Sigma-Aldrich) with 10% PEG2000 in 100mM Sodium Phosphate buffer, pH=7.0, c=5mg/ml

Hemoglobin subunit alphaHemoglobin subunit betaProtoporphyrin IX containing fe experimental SAS data
DAMMIF model
Sample: Hemoglobin subunit alpha monomer, 15 kDa Homo sapiens protein
Hemoglobin subunit beta monomer, 16 kDa Homo sapiens protein
Protoporphyrin IX containing fe monomer, 1 kDa
Buffer: 100mM Sodium Phosphate buffer with 10% (w/v) PEG2000, pH: 7
Experiment: SAXS data collected at Anton Paar SAXSpoint 2.0, Institute of Biotechnology, Czech Academy of Sciences/Centre of Molecular Structure on 2022 Oct 6
Hemoglobin–PEG Interactions Probed by Small-Angle X-ray Scattering: Insights for Crystallization and Diagnostics Applications The Journal of Physical Chemistry B (2024)
Baranova I, Angelova A, Stransky J, Andreasson J, Angelov B
RgGuinier 2.8 nm
Dmax 11.3 nm
VolumePorod 131 nm3

SASDVZ5 – Human DNA repair protein RAD52 homolog (amino acids 1-212)

DNA repair protein RAD52 homolog experimental SAS data
DAMMIF model
Sample: DNA repair protein RAD52 homolog decamer, 234 kDa Homo sapiens protein
Buffer: 20 mM Bis-Tris, 10% glycerol, 400 mM NaCl, 100 mM KCl, 1 mM EDTA, pH: 6
Experiment: SAXS data collected at Rigaku BioSAXS 1000, Eppley Structural Biology Facility, University of Nebraska Medical Center on 2014 Jul 25
A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52 Journal of Structural Biology 216(3):108115 (2024)
Struble L, Lovelace J, Borgstahl G
RgGuinier 4.1 nm
Dmax 11.8 nm
VolumePorod 375 nm3

SASDV26 – Human DNA repair protein RAD52 homolog (amino acids 1-303)

DNA repair protein RAD52 homolog experimental SAS data
DAMMIF model
Sample: DNA repair protein RAD52 homolog nonamer, 300 kDa Homo sapiens protein
Buffer: 20 mM Bis-Tris, 10% GLycerol, 400 mM NaCl, 100 mM KCl, 1mM EDTA, pH: 6
Experiment: SAXS data collected at Rigaku BioSAXS 1000, Eppley Structural Biology Facility, University of Nebraska Medical Center on 2014 Jul 25
A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52 Journal of Structural Biology 216(3):108115 (2024)
Struble L, Lovelace J, Borgstahl G
RgGuinier 4.8 nm
Dmax 18.3 nm
VolumePorod 782 nm3