Browse by MODEL: Ab initio only

SASDUD2 – mTIP120-Ba (metal-ion induced 120-mer complex of TIP120 mutant (K26E in C-terminal subunit) with Ba ions)

N-terminal split fragment of a single subunit of Truncated Icosahedral Protein composed of 60-mer fusion proteinsK26E mutant of C-terminal split fragment of a single subunit of Truncated Icosahedral Protein composed of 60-mer fusion proteins experimental SAS data
DAMMIN model
Sample: N-terminal split fragment of a single subunit of Truncated Icosahedral Protein composed of 60-mer fusion proteins, 360 kDa synthetic construct protein
K26E mutant of C-terminal split fragment of a single subunit of Truncated Icosahedral Protein composed of 60-mer fusion proteins, 857 kDa synthetic construct protein
Buffer: 25 mM HEPES, 100 mM NaCl, 4 mM BaCl2, 5%(v/v) glycerol, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2023 Nov 27
Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) (2024)
Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K
RgGuinier 9.4 nm
Dmax 22.4 nm
VolumePorod 3320 nm3

SASDGZ9 – Protein Disulfide Isomerase (PDI) purified from bovine liver

Protein disulfide-isomerase experimental SAS data
DAMMIF model
Sample: Protein disulfide-isomerase monomer, 57 kDa Bos taurus protein
Buffer: 50 mM Tris-HCL, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Nov 4
Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique In Silico Pharmacology 12(1) (2024)
Sanyasi C, Balakrishnan S, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel S
RgGuinier 3.0 nm
Dmax 9.8 nm
VolumePorod 98 nm3

SASDH22 – Protein Disulfide Isomerase (PDI) in complex with Bovine Pancreatic Trypsin Inhibitor (BPTI)

Protein disulfide-isomerasePancreatic trypsin inhibitor experimental SAS data
DAMMIF model
Sample: Protein disulfide-isomerase monomer, 57 kDa Bos taurus protein
Pancreatic trypsin inhibitor monomer, 7 kDa Bos taurus protein
Buffer: 50 mM Tris-HCL, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Nov 4
Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique In Silico Pharmacology 12(1) (2024)
Sanyasi C, Balakrishnan S, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel S
RgGuinier 3.2 nm
Dmax 8.9 nm
VolumePorod 88 nm3

SASDH32 – Protein Disulfide Isomerase (PDI) in Complex with Ribonuclease-A (RNase)

Protein disulfide-isomeraseRibonuclease pancreatic experimental SAS data
DAMMIF model
Sample: Protein disulfide-isomerase monomer, 57 kDa Bos taurus protein
Ribonuclease pancreatic monomer, 14 kDa Bos taurus protein
Buffer: 50 mM Tris-HCL, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Nov 4
Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique In Silico Pharmacology 12(1) (2024)
Sanyasi C, Balakrishnan S, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel S
RgGuinier 3.0 nm
Dmax 9.1 nm
VolumePorod 85 nm3

SASDH42 – Bovine Pancreatic Trypsin Inhibitor (BPTI) in solution environment at pH 7.5

Pancreatic trypsin inhibitor experimental SAS data
DAMMIF model
Sample: Pancreatic trypsin inhibitor dimer, 13 kDa Bos taurus protein
Buffer: 50 mM Tris-HCL, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Nov 4
Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique In Silico Pharmacology 12(1) (2024)
Sanyasi C, Balakrishnan S, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel S
RgGuinier 1.4 nm
Dmax 4.6 nm
VolumePorod 6 nm3

SASDH52 – Ribonuclease A (Type III-A) in a solution environment at pH 7.5

Ribonuclease pancreatic experimental SAS data
DAMMIF model
Sample: Ribonuclease pancreatic monomer, 14 kDa Bos taurus protein
Buffer: 50 mM Tris-HCL, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2015 Nov 4
Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique In Silico Pharmacology 12(1) (2024)
Sanyasi C, Balakrishnan S, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel S
RgGuinier 1.9 nm
Dmax 7.2 nm
VolumePorod 20 nm3

SASDUS3 – Dark-adapted photocobilin diguanylate cyclase fusion from Acidimicrobiaceae bacterium

GGDEF domain-containing protein experimental SAS data
DAMMIF model
Sample: GGDEF domain-containing protein dimer, 132 kDa Acidimicrobiaceae bacterium protein
Buffer: 20 mM HEPES, 150 mM NaCl, pH: 6.8
Experiment: SAXS data collected at BM29, ESRF on 2022 Jan 21
Photocobilins integrate B(12) and bilin photochemistry for enzyme control. Nat Commun 15(1):2740 (2024)
Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schirò G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS
RgGuinier 4.1 nm
Dmax 14.9 nm
VolumePorod 194 nm3

SASDUT3 – Light-adapted photocobilin diguanylate cyclase fusion from Acidimicrobiaceae bacterium

GGDEF domain-containing protein experimental SAS data
DAMMIF model
Sample: GGDEF domain-containing protein dimer, 132 kDa Acidimicrobiaceae bacterium protein
Buffer: 20 mM HEPES, 150 mM NaCl, pH: 6.8
Experiment: SAXS data collected at BM29, ESRF on 2022 Jan 21
Photocobilins integrate B(12) and bilin photochemistry for enzyme control. Nat Commun 15(1):2740 (2024)
Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schirò G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS
RgGuinier 5.0 nm
Dmax 18.5 nm
VolumePorod 170 nm3

SASDKW6 – SARS-CoV-2 non-structural protein 10/non-structural protein 14/non-structural protein 16 triplex (nsp10/nsp14/nsp16)

Replicase polyprotein 1ab (non-structural protein 14)Replicase polyprotein 1a (non-structural protein 10)Replicase polyprotein 1ab (non-structural protein 16) experimental SAS data
GASBOR model
Sample: Replicase polyprotein 1ab (non-structural protein 14) monomer, 60 kDa Severe acute respiratory … protein
Replicase polyprotein 1a (non-structural protein 10) monomer, 15 kDa Severe acute respiratory … protein
Replicase polyprotein 1ab (non-structural protein 16) monomer, 33 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 150 mM NaCl, 5 mM MgCl2, 2 mM β-mercaptoethanol, pH: 8.5
Experiment: SAXS data collected at BM29, ESRF on 2020 Dec 11
Despite the odds: formation of the SARS-CoV-2 methylation complex Nucleic Acids Research (2024)
Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones A, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz G, Pyrć K, Czarna A
RgGuinier 4.7 nm
Dmax 11.4 nm
VolumePorod 113 nm3

SASDSY8 – S9C peptidase from Geobacillus stearothermophilus

Acylamino-acid-releasing enzyme (I277L, V491A) experimental SAS data
GASBOR model
Sample: Acylamino-acid-releasing enzyme (I277L, V491A) tetramer, 308 kDa Geobacillus stearothermophilus protein
Buffer: 10 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BL-18, INDUS-2 on 2023 Aug 11
Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Lett (2024)
Chandravanshi K, Singh R, Bhange GN, Kumar A, Yadav P, Kumar A, Makde RD
RgGuinier 5.3 nm
Dmax 13.0 nm
VolumePorod 424 nm3