Browse by MODEL: Hybrid

SASDQ69 – 28 base pair DNA substrate (used in experiments with 7-deazapurine in DNA proteins)

Custom 28 base pair double stranded DNA experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.6 nm
Dmax 10.2 nm
VolumePorod 24 nm3

SASDQ79 – Mutant 7-deazapurine in DNA protein A (D95A) bound to a 28 base pair DNA substrate (2-state model: complex plus free DNA)

Custom 28 base pair double stranded DNADNA-guanine transglycosylase - D95A mutant experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
DNA-guanine transglycosylase - D95A mutant monomer, 50 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 104 nm3

SASDQ89 – 7-deazapurine in DNA protein B

DGQHR domain-containing protein experimental SAS data
ALPHAFOLD model
Sample: DGQHR domain-containing protein dimer, 88 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 126 nm3

SASDRW6 – YdaS, a cro-type repressor from Escherichai coli O157:H7 cryptic prophage CP-933

Phage antirepressor protein Cro experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Phage antirepressor protein Cro monomer, 12 kDa Escherichia coli O157:H7 protein
Buffer: 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH: 5.5
Experiment: SAXS data collected at SWING, SOLEIL on 2018 Feb 5
Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7
Marusa Prolic Kalinsek
RgGuinier 2.1 nm
Dmax 7.6 nm
VolumePorod 19 nm3

SASDP28 – Growth factor receptor-bound protein 2 (GRB2) - wild-type monomer

Growth factor receptor-bound protein 2 experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 monomer, 28 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 2.5 nm
Dmax 9.0 nm
VolumePorod 40 nm3

SASDP38 – Growth factor receptor-bound protein 2 (GRB2) - wild-type dimer

Growth factor receptor-bound protein 2 experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 dimer, 55 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 3.7 nm
Dmax 14.0 nm
VolumePorod 110 nm3

SASDP48 – Growth factor receptor-bound protein 2 (GRB2) - N188D/N214D mutant monomer

Growth factor receptor-bound protein 2 (N188D, N214D) experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 (N188D, N214D) monomer, 28 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 2.5 nm
Dmax 9.5 nm
VolumePorod 39 nm3

SASDP58 – Growth factor receptor-bound protein 2 (GRB2) - N188D/N214D mutant dimer

Growth factor receptor-bound protein 2 (N188D, N214D) experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 (N188D, N214D) dimer, 55 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 4.1 nm
Dmax 15.0 nm
VolumePorod 140 nm3

SASDP68 – Growth factor receptor-bound protein 2 (GRB2) - V123D mutant monomer

Growth factor receptor-bound protein 2 (V123D) experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 (V123D) monomer, 28 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 2.6 nm
Dmax 10.0 nm
VolumePorod 45 nm3

SASDP78 – Growth factor receptor-bound protein 2 (GRB2) - V122P/V123P mutant dimer

Growth factor receptor-bound protein 2 (V122P, V123P) experimental SAS data
PYMOL model
Sample: Growth factor receptor-bound protein 2 (V122P, V123P) dimer, 55 kDa Homo sapiens protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 31
GRB2 dimerization mediated by SH2 domain-swapping is critical for T cell signaling and cytokine production. Sci Rep 13(1):3505 (2023)
Sandouk A, Xu Z, Baruah S, Tremblay M, Hopkins JB, Chakravarthy S, Gakhar L, Schnicker NJ, Houtman JCD
RgGuinier 3.7 nm
Dmax 20.4 nm
VolumePorod 85 nm3