Browse by MODEL: Hybrid

SASDP29 – Gli-55 - ssDNA aptamer specific to glioma brain tumor cells

Gli-55 - ssDNA aptamer specific to glioma brain tumor cells experimental SAS data
DAMMIN model
Sample: Gli-55 - ssDNA aptamer specific to glioma brain tumor cells monomer, 19 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 30
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 2.8 nm
Dmax 11.5 nm
VolumePorod 34 nm3

SASDRY7 – Gli-55 - ssDNA aptamer to glioma brain tumor cells

Gli-55 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
DAMMIF model
Sample: Gli-55 - ssDNA aptamer to glioma brain tumor cells monomer, 19 kDa synthetic construct DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS), pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Oct 30
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 2.8 nm
Dmax 11.5 nm
VolumePorod 35 nm3

SASDQE9 – YdaT_toxin domain-containing protein bound to 30 base pair dsDNA

YdaT_toxin domain-containing proteinOm 30 base pair dsDNA experimental SAS data
OTHER model
Sample: YdaT_toxin domain-containing protein tetramer, 74 kDa Escherichia coli O157:H7 protein
Om 30 base pair dsDNA dimer, 37 kDa DNA
Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 14
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7 Acta Crystallographica Section D Structural Biology 79(3):245-258 (2023)
Prolič-Kalinšek M, Volkov A, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R
RgGuinier 4.2 nm
Dmax 12.8 nm
VolumePorod 190 nm3

SASDPB6 – Fibronectin 2 and 3 of cell adhesion molecule L1 (L1CAM) expressed in HEK293S GnTI-

Neural cell adhesion molecule L1 experimental SAS data
DAMMIN model
Sample: Neural cell adhesion molecule L1 monomer, 24 kDa Homo sapiens protein
Buffer: 50 mM MES pH 6.5, 150 mM NaCl, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 May 11
X‐ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1 The FASEB Journal 37(3) (2023)
Guédez G, Loers G, Jeffries C, Kozak S, Meijers R, Svergun D, Schachner M, Löw C
RgGuinier 2.8 nm
Dmax 9.5 nm
VolumePorod 68 nm3

SASDPC6 – Fibronectin 2 and 3 of cell adhesion molecule L1 (L1CAM) expressed in HEK293F

Neural cell adhesion molecule L1 experimental SAS data
DAMMIN model
Sample: Neural cell adhesion molecule L1 monomer, 24 kDa Homo sapiens protein
Buffer: 50 mM MES pH 6.5, 150 mM NaCl, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 May 11
X‐ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1 The FASEB Journal 37(3) (2023)
Guédez G, Loers G, Jeffries C, Kozak S, Meijers R, Svergun D, Schachner M, Löw C
RgGuinier 2.9 nm
Dmax 9.9 nm
VolumePorod 72 nm3

SASDPD6 – Fibronectin 2 and 3 of cell adhesion molecule L1 (L1CAM) expressed in HEK293F cells with kifunensine

Neural cell adhesion molecule L1 experimental SAS data
CORAL model
Sample: Neural cell adhesion molecule L1 monomer, 24 kDa Homo sapiens protein
Buffer: 50 mM MES pH 6.5, 150 mM NaCl, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 May 11
X‐ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1 The FASEB Journal 37(3) (2023)
Guédez G, Loers G, Jeffries C, Kozak S, Meijers R, Svergun D, Schachner M, Löw C
RgGuinier 2.9 nm
Dmax 9.6 nm
VolumePorod 72 nm3

SASDD73 – Flavin reductase Pden_5119

NADPH-dependent FMN reductase experimental SAS data
SWISSMODEL model
Sample: NADPH-dependent FMN reductase dimer, 41 kDa Paracoccus denitrificans protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 Feb 22
Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans. Int J Mol Sci 24(4) (2023)
Kryl M, Sedláček V, Kučera I
RgGuinier 2.3 nm
Dmax 6.3 nm
VolumePorod 70 nm3

SASDKE6 – Poly(A) polymerase pla1 bound to the NURS complex subunit red1

NURS complex subunit red1Poly(A) polymerase pla1 experimental SAS data
CORAL model
Sample: NURS complex subunit red1 monomer, 8 kDa Schizosaccharomyces pombe (strain … protein
Poly(A) polymerase pla1 monomer, 65 kDa Schizosaccharomyces pombe (strain … protein
Buffer: 20 mM HEPES, pH 7.5, 150 mM NaCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nat Commun 14(1):772 (2023)
Soni K, Sivadas A, Horvath A, Dobrev N, Hayashi R, Kiss L, Simon B, Wild K, Sinning I, Fischer T
RgGuinier 3.3 nm
Dmax 10.7 nm
VolumePorod 138 nm3

SASDQN4 – Complex of CRISPR associated Lon protease (CalpL) with a 10 kDa C-terminal fragment of CalpT a putative MazF-like toxin (CalpT10)

SAVED domain-containing proteinUncharacterized protein (putative MazF-like toxin) experimental SAS data
CUSTOM IN-HOUSE model
Sample: SAVED domain-containing protein monomer, 58 kDa Sulfurihydrogenibium sp. (strain … protein
Uncharacterized protein (putative MazF-like toxin) monomer, 9 kDa Sulfurihydrogenibium sp. (strain … protein
Buffer: 20 mM Tris, 50 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Dec 14
Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 614(7946):168-174 (2023)
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G
RgGuinier 3.4 nm
Dmax 11.7 nm
VolumePorod 93 nm3

SASDRS2 – Collagen-like peptide Mannan-binding lectin (MBL) center

Ac-(POG)4-QG-(POG)5-NH2 experimental SAS data
PYMOL model
Sample: Ac-(POG)4-QG-(POG)5-NH2 trimer, 11 kDa synthetic construct protein
Buffer: 20 mM L-histidine, 138 mM NaCl, 2.7 mM KCL,, pH: 6
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Feb 1
A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin. J Biol Chem 299(2):102799 (2023)
Iqbal H, Fung KW, Gor J, Bishop AC, Makhatadze GI, Brodsky B, Perkins SJ
RgGuinier 2.1 nm
Dmax 8.7 nm
VolumePorod 7 nm3