Browse by MODEL: Hybrid

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

SASDP74 – AT-rich DNA

AT-rich dsDNA experimental SAS data
DAMMIN model
Sample: AT-rich dsDNA monomer, 7 kDa DNA
Buffer: 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 6
Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome. Life Sci Alliance 6(3) (2023)
Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG
RgGuinier 1.7 nm
Dmax 4.6 nm
VolumePorod 12 nm3

SASDPZ8 – Gli-233 - ssDNA aptamer specific to glioma brain tumor cells

Gli-233 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
GROMACS model
Sample: Gli-233 - ssDNA aptamer to glioma brain tumor cells monomer, 10 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS, with Ca and Mg), pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 17
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
Kichkailo A, Narodov A, Komarova M, Zamay T, Zamay G, Kolovskaya O, Erakhtin E, Glazyrin Y, Veprintsev D, Moryachkov R, Zabluda V, Shchugoreva I, Artyushenko P, Mironov V, Morozov D, Khorzhevskii V, Gorbushin A, Koshmanova A, Nikolaeva E, Grinev I, Voronkovskii I, Grek D, Belugin K, Volzhentsev A, Badmaev O, Luzan N, Lukyanenko K, Peters G, Lapin I, Kirichenko A, Konarev P, Morozov E, Mironov G, Gargaun A, Muharemagic D, Zamay S, Kochkina E, Dymova M, Smolyarova T, Sokolov A, Modestov A, Tokarev N, Shepelevich N, Ozerskaya A, Chanchikova N, Krat A, Zukov R, Bakhtina V, Shnyakin P, Shesternya P, Svetlichnyi V, Petrova M, Artyukhov I, Tomilin F, Berezovski M
RgGuinier 1.9 nm
Dmax 6.8 nm
VolumePorod 13 nm3