Browse by MODEL: Ab initio only

SASDUB2 – The Z-DNA binding domains Zαβ of Z-DNA binding protein 1 (dimer)

Z-DNA-binding protein 1 experimental SAS data
DAMMIF model
Sample: Z-DNA-binding protein 1 dimer, 37 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
ZBP1 condensate formation synergizes Z-NAs recognition and signal transduction. Cell Death Dis 15(7):487 (2024)
Xie F, Wu D, Huang J, Liu X, Shen Y, Huang J, Su Z, Li J
RgGuinier 3.1 nm
Dmax 13.0 nm
VolumePorod 48 nm3

SASDSP7 – 5’-terminal stem-loop 1 RNA element of SARS-CoV-2 (5_SL1)

5_SL1 experimental SAS data
DAMMIN model
Sample: 5_SL1 monomer, 9 kDa Severe acute respiratory … RNA
Buffer: 50 mM BisTris, 25 mM NaCl, pH: 6.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Dec 1
The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH. Nucleic Acids Res (2024)
Toews S, Wacker A, Faison EM, Duchardt-Ferner E, Richter C, Mathieu D, Bottaro S, Zhang Q, Schwalbe H
RgGuinier 1.7 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDPP7 – Amyloid Beta 1-42 (cluster 1, Set 2, final state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.12 % NH4OH, pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Apr 11
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 5.8 nm
Dmax 42.0 nm

SASDPQ7 – Amyloid Beta 1-42 (cluster 1, Set 3, final state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.12 % NH4OH, pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 13
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 6.9 nm
Dmax 60.0 nm

SASDPR7 – Amyloid Beta 1-42 (cluster 2, Set 4, initial state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.1 % NH4OH (pH∼10.7), pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Oct 31
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 2.5 nm
Dmax 6.5 nm

SASDPS7 – Amyloid Beta 1-42 (cluster 2, Set 4, final state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.1 % NH4OH (pH∼10.7), pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Nov 1
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 3.7 nm
Dmax 9.1 nm

SASDPT7 – Amyloid Beta 1-42 (cluster 2, Set 5, final state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.1 % NH4OH (pH∼10.7), pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Nov 1
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 3.7 nm
Dmax 11.0 nm

SASDPU7 – Amyloid Beta 1-42 (cluster 1, Set 1, initial state)

Amyloid-beta precursor protein experimental SAS data
DAMMIN model
Sample: Amyloid-beta precursor protein, 5 kDa Homo sapiens protein
Buffer: 1 mM Hepes, 0.12 % NH4OH, pH: 10.7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 2
Time-resolved small-angle X-ray scattering study of polymorphic nature of Aß42 oligomerisation
Tia Cheremnykh
RgGuinier 3.5 nm
Dmax 15.0 nm

SASDPE3 – GST-Endonuclease 8 2/Single-stranded DNA-binding protein (Nei2-SSB) complex

Endonuclease 8 2Single-stranded DNA-binding protein experimental SAS data
DAMMIF model
Sample: Endonuclease 8 2 dimer, 108 kDa Mycobacterium tuberculosis (strain … protein
Single-stranded DNA-binding protein octamer, 139 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Jul 10
Identification and characterization of MtbNei2-SSB forms novel pre-replicative BER complex in Mycobacterium tuberculosis.
Jyoti Vishwakarma
RgGuinier 5.5 nm
Dmax 21.0 nm
VolumePorod 734 nm3

SASDUX7 – Aspergillus niger beta-glucosidase (bgl1), partially deglycosylated with Endoglycosidase H

beta-glucosidase experimental SAS data
GASBOR model
Sample: Beta-glucosidase dimer, 187 kDa Aspergillus niger protein
Buffer: 50 mM sodium acetate, pH: 5
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2024 Feb 15
Aspergillus niger beta-glucosidase (bgl1)
Estella Yee
RgGuinier 4.2 nm
Dmax 14.0 nm
VolumePorod 253 nm3