Browse by MODEL: Hybrid

SASDAC7 – Complex LytTR-comcde

comcdeResponse regulator experimental SAS data
SASREF model
Sample: Comcde, 24 kDa Streptococcus pneumoniae DNA
Response regulator dimer, 29 kDa Streptococcus pneumoniae protein
Buffer: 50 mM MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol, pH: 6.2
Experiment: SAXS data collected at SWING, SOLEIL on 2013 Jun 2
Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering. FEBS J 282(8):1538-53 (2015)
Sanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S
RgGuinier 3.6 nm
Dmax 12.5 nm
VolumePorod 74 nm3

SASDLG5 – Human nerve growth factor

Beta-nerve growth factor experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Beta-nerve growth factor dimer, 24 kDa Homo sapiens protein
Buffer: 50 mM Na-phosphate, 1 mM EDTA, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2007 Jul 2
The conundrum of the high-affinity NGF binding site formation unveiled? Biophys J 108(3):687-97 (2015)
Covaceuszach S, Konarev PV, Cassetta A, Paoletti F, Svergun DI, Lamba D, Cattaneo A
RgGuinier 2.5 nm

SASDL57 – Thermus thermophilus 3-isopropylmalate dehydrogenase

3-isopropylmalate dehydrogenase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: 3-isopropylmalate dehydrogenase dimer, 73 kDa Thermus thermophilus protein
Buffer: 25 mM MOPS/NaOH, pH: 7.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 3
Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase. FEBS Lett 589(2):240-5 (2015)
Gráczer É, Palló A, Oláh J, Szimler T, Konarev PV, Svergun DI, Merli A, Závodszky P, Weiss MS, Vas M
RgGuinier 2.8 nm

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)
Tallant C, 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)
Tallant C, 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

SASDAH6 – WbdD(1-459)

bifunctional kinase- methyltransferase WbdD experimental SAS data
CORAL model
Sample: Bifunctional kinase- methyltransferase WbdD monomer, 59 kDa Escherichia coli protein
Buffer: 20 mM BisTris 50 mM NaCl 5 mM DTT, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Sep 23
A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat Struct Mol Biol 22(1):50-56 (2015)
Hagelueken G, Clarke BR, Huang H, Tuukkanen A, Danciu I, Svergun DI, Hussain R, Liu H, Whitfield C, Naismith JH
RgGuinier 3.1 nm
Dmax 10.0 nm
VolumePorod 90 nm3

SASDAJ6 – WbdD(1-556)

bifunctional kinase- methyltransferase WbdD experimental SAS data
CORAL model
Sample: Bifunctional kinase- methyltransferase WbdD trimer, 190 kDa protein
Buffer: 20 mM BisTris 50 mM NaCl 5 mM DTT, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 2
A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat Struct Mol Biol 22(1):50-56 (2015)
Hagelueken G, Clarke BR, Huang H, Tuukkanen A, Danciu I, Svergun DI, Hussain R, Liu H, Whitfield C, Naismith JH
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 380 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)
Mittelberger F, Meyer C, Waetzig GH, Zacharias M, 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

SASDLP5 – Complex of the josephin domain of ataxin-3 with ubiquitin

Josephin domain of ataxin-3Polyubiquitin-B experimental SAS data
DAMMIF model
Sample: Josephin domain of ataxin-3 monomer, 21 kDa Homo sapiens protein
Polyubiquitin-B monomer, 9 kDa Homo sapiens protein
Buffer: 20 mM Na-phosphate, 2 mM DTT, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Oct 7
Allosteric regulation of deubiquitylase activity through ubiquitination. Front Mol Biosci 2:2 (2015)
Faggiano S, Menon RP, Kelly GP, Todi SV, Scaglione KM, Konarev PV, Svergun DI, Paulson HL, Pastore A
RgGuinier 2.1 nm
Dmax 6.5 nm
VolumePorod 45 nm3

SASDLH3 – Truncated Thermoplasma E2 catalytic core

Regulatory protein E2 experimental SAS data
CUSTOM IN-HOUSE model
Sample: Regulatory protein E2 trimer, 73 kDa Human papillomavirus type … protein
Buffer: 50 mM Tris ⁄ HCl, pH 8.8, 100 mM NaCl, pH: 8.8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 May 27
Why are the 2-oxoacid dehydrogenase complexes so large? Generation of an active trimeric complex Biochemical Journal 463(3):405-412 (2014)
Marrott N, Marshall J, Svergun D, Crennell S, Hough D, van den Elsen J, Danson M
RgGuinier 3.1 nm
Dmax 11.0 nm
VolumePorod 149 nm3