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18 hits found for Valentini

SASDA46 – TIP5 in Tris

Bromodomain adjacent to zinc finger domain protein 2A experimental SAS data
BUNCH model
Sample: Bromodomain adjacent to zinc finger domain protein 2A monomer, 27 kDa Homo sapiens protein
Buffer: 20 mM Tris 500 mM NaCl 2 mM DTT 10 microM ZnCl2, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Mar 16
Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 23(1):80-92 (2015)
...Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A
RgGuinier 3.0 nm
Dmax 10.0 nm
VolumePorod 45 nm3

SASDA56 – BAZ2B in Tris

Bromodomain adjacent to zinc finger domain protein 2B, C-terminal experimental SAS data
EOM/RANCH model
Sample: Bromodomain adjacent to zinc finger domain protein 2B, C-terminal monomer, 28 kDa Homo sapiens protein
Buffer: 20 mM Tris 500 mM NaCl 2 mM DTT 10 microM ZnCl2, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2012 Sep 24
Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 23(1):80-92 (2015)
...Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A
RgGuinier 4.0 nm
Dmax 14.5 nm
VolumePorod 43 nm3

SASDA66 – BAZ2B-18mer complex in Tris

Bromodomain adjacent to zinc finger domain protein 2B, C-terminalH3Kac9Kac14 experimental SAS data
Bromodomain adjacent to zinc finger domain protein 2B, C-terminal H3Kac9Kac14 Kratky plot
Sample: Bromodomain adjacent to zinc finger domain protein 2B, C-terminal monomer, 28 kDa Homo sapiens protein
H3Kac9Kac14 monomer, 5 kDa Homo sapiens protein
Buffer: 20 mM Tris 500 mM NaCl 2 mM DTT 10 microM ZnCl2, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2012 Sep 24
Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 23(1):80-92 (2015)
...Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A
RgGuinier 4.2 nm
Dmax 16.0 nm
VolumePorod 52 nm3

SASDAK6 – Glucose Isomerase

Xylose isomerase experimental SAS data
DAMMIF model
Sample: Xylose isomerase tetramer, 172 kDa Streptomyces rubiginosus protein
Buffer: PBS, 50% Glycerol, 0.076 M NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2012 Apr 24
Standard proteins
Erica Valentini
RgGuinier 3.4 nm
Dmax 9.7 nm
VolumePorod 293 nm3

SASDAP7 – PBX1-PREB1 complex

Pre-B-cell leukemia transcription factor 1Homeobox protein PKNOX1 experimental SAS data
DAMMIF model
Sample: Pre-B-cell leukemia transcription factor 1 monomer, 34 kDa Homo sapiens protein
Homeobox protein PKNOX1 monomer, 38 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 283(16):3134-54 (2016)
...Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C
RgGuinier 5.8 nm
Dmax 19.0 nm
VolumePorod 143 nm3

SASDAQ7 – PBX1-PREB1-DNA complex

Pre-B-cell leukemia transcription factor 1Homeobox protein PKNOX1DNA 22mer experimental SAS data
DAMMIF model
Sample: Pre-B-cell leukemia transcription factor 1 monomer, 34 kDa Homo sapiens protein
Homeobox protein PKNOX1 monomer, 38 kDa Homo sapiens protein
DNA 22mer monomer, 12 kDa DNA
Buffer: 20 mM Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 283(16):3134-54 (2016)
...Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C
RgGuinier 4.8 nm
Dmax 16.3 nm
VolumePorod 173 nm3

SASDAR7 – DNA 22mer

DNA 22mer experimental SAS data
DAMMIF model
Sample: DNA 22mer monomer, 12 kDa DNA
Buffer: 20 mM Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 283(16):3134-54 (2016)
...Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C
RgGuinier 2.2 nm
Dmax 7.5 nm
VolumePorod 19 nm3

SASDAT7 – Aptamer AIR-3 5FU

AIR3-5FU experimental SAS data
DAMMIF model
Sample: AIR3-5FU dimer, 69 kDa RNA
Buffer: water, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Oct 31
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 4.3 nm
Dmax 16.0 nm
VolumePorod 77 nm3

SASDAU7 – Aptamer AIR-3 FdU

AIR3-FdU experimental SAS data
DAMMIF model
Sample: AIR3-FdU dimer, 69 kDa RNA
Buffer: water, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Oct 31
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 5.0 nm
Dmax 16.0 nm
VolumePorod 67 nm3

SASDAV7 – Aptamer AIR-3A

AIR-3A experimental SAS data
DAMMIN model
Sample: AIR-3A dimer, 13 kDa RNA
Buffer: water, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 1.9 nm
Dmax 6.5 nm
VolumePorod 14 nm3

SASDAW7 – Aptamer AIR-3A 2'FU

AIR-3A 2'FU experimental SAS data
AIR-3A 2'FU Kratky plot
Sample: AIR-3A 2'FU dimer, 13 kDa RNA
Buffer: water, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 1.9 nm
Dmax 6.0 nm
VolumePorod 12 nm3

SASDAX7 – Aptamer AIR-3A G18U

AIR-3A G18U experimental SAS data
AIR-3A G18U Kratky plot
Sample: AIR-3A G18U tetramer, 25 kDa RNA
Buffer: water, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 6
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 2.5 nm
Dmax 8.3 nm
VolumePorod 24 nm3

SASDAY7 – IL-6R tetramer-dimer equilibrium

Interleukin-6 receptor subunit alphaInterleukin-6 receptor subunit alpha experimental SAS data
CORAL model
Sample: Interleukin-6 receptor subunit alpha tetramer, 164 kDa Homo sapiens protein
Interleukin-6 receptor subunit alpha dimer, 82 kDa Homo sapiens protein
Buffer: water, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2014 Oct 1
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 4.9 nm
Dmax 20.0 nm
VolumePorod 240 nm3

SASDAZ7 – IL-6R AIR-3A 2:4 complex

AIR-3AInterleukin-6 receptor subunit alpha experimental SAS data
DAMMIF model
Sample: AIR-3A tetramer, 26 kDa RNA
Interleukin-6 receptor subunit alpha dimer, 82 kDa Homo sapiens protein
Buffer: water, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2014 Oct 1
Structure and target interaction of a G-quadruplex RNA-aptamer. RNA Biol 13(10):973-987 (2016)
...Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
RgGuinier 6.7 nm
Dmax 25.0 nm
VolumePorod 150 nm3

SASDA88 – RAID3 in PBS

RAID3 experimental SAS data
DAMMIN model
Sample: RAID3 dimer, 23 kDa RNA
Buffer: PBS 137 mM NaCl 2,7 mM KCl 6,5 mM Na2HPO4 1,5 mM KH2PO4, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2013 Oct 31
RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity. RNA Biol 12(9):1043-53 (2015)
...Valentini E, Svergun DI, Berg K, Lorenzen I, Grötzinger J, Rose-John S, Hahn U
RgGuinier 2.7 nm
Dmax 10.0 nm
VolumePorod 26 nm3

SASDKV9 – Transcription factors USF1 and NF-Y bound to a CCAAT DNA box(48bp)

Upstream stimulatory factor 1Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
CORAL model
Sample: Upstream stimulatory factor 1 dimer, 50 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 14
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
...Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 155 nm3

SASDKW9 – Transcription factors USF1 and NF-Y bound to a CCAAT DNA box(50bp)

Upstream stimulatory factor 1Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 50bp experimental SAS data
DAMMIN model
Sample: Upstream stimulatory factor 1 dimer, 50 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 50bp monomer, 31 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 14
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
...Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 165 nm3

SASDKX9 – Transcription factors MAX and NF-Y bound to a CCAAT DNA box(48bp)

Protein max (Isoform 2, short, 13-21: missing)Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
DAMMIN model
Sample: Protein max (Isoform 2, short, 13-21: missing) dimer, 39 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2012 Dec 10
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
...Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 151 nm3