Browse by MODEL: Hybrid

SASDMA9 – Diacetylchitobiose deacetylase (isolated hexamer from SEC-SAXS)

Diacetylchitobiose deacetylase experimental SAS data
PYMOL model
Sample: Diacetylchitobiose deacetylase hexamer, 186 kDa Thermococcus chitonophagus protein
Buffer: 20 mM TRIS, 200 mM NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Sep 26
Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Int J Mol Sci 23(24) (2022)
Biniek-Antosiak K, Bejger M, Śliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W
RgGuinier 3.6 nm
Dmax 11.2 nm
VolumePorod 317 nm3

SASDMB9 – Diacetylchitobiose deacetylase (oligomeric mixture of hexamers and dodecamers)

Diacetylchitobiose deacetylase experimental SAS data
PYMOL model
Sample: Diacetylchitobiose deacetylase, 185 kDa Thermococcus chitonophagus protein
Buffer: 20 mM TRIS, 200 mM NaCl, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Sep 26
Structural, Thermodynamic and Enzymatic Characterization of N,N-Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Int J Mol Sci 23(24) (2022)
Biniek-Antosiak K, Bejger M, Śliwiak J, Baranowski D, Mohammed ASA, Svergun DI, Rypniewski W
RgGuinier 3.9 nm

SASDMH7 – ESX-1 secretion-associated protein EspB medium construct bound to ESX-1 secretion-associated protein EspK — EspBM-K complex

ESX-1 secretion-associated protein EspKESX-1 secretion-associated protein EspB experimental SAS data
CORAL model
Sample: ESX-1 secretion-associated protein EspK monomer, 27 kDa Mycobacterium tuberculosis (strain … protein
ESX-1 secretion-associated protein EspB monomer, 37 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris-HCl, 300 mM NaCl, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Apr 12
The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in M. tuberculosis. J Biol Chem :102761 (2022)
Gijsbers A, Eymery M, Gao Y, Menart I, Vinciauskaite V, Siliqi D, Peters PJ, McCarthy A, Ravelli RBG
RgGuinier 4.3 nm
Dmax 15.7 nm
VolumePorod 100 nm3

SASDMH9 – Pseudomonas aeruginosa Multidrug resistance operon repressor (MexR) in complex with 34bp dsDNA binding sequence (SANS data at 0% D2O)

Multidrug resistance operon repressor34 base pair double-stranded DNA experimental SAS data
MONSA model
Sample: Multidrug resistance operon repressor dimer, 32 kDa Pseudomonas aeruginosa protein
34 base pair double-stranded DNA monomer, 21 kDa synthetic construct DNA
Buffer: 20mM NaPO4, 150 mM NaCl, 10 mM DTT, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2018 May 30
Small-angle X-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model Biophysical Journal (2022)
Caporaletti F, Pietras Z, Morad V, Mårtensson L, Gabel F, Wallner B, Martel A, Sunnerhagen M
RgGuinier 2.9 nm
Dmax 7.8 nm
VolumePorod 79 nm3

SASDPY6 – BTB domain of longitudinals lacking protein (LOLA) at 1.0 mg/ml

Longitudinals lacking protein, isoform G experimental SAS data
ALPHAFOLD model
Sample: Longitudinals lacking protein, isoform G hexamer, 92 kDa Drosophila melanogaster protein
Buffer: 20 mM Tris, pH 7.4, 200 mM NaCl, 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jul 8
BTB domains: A structural view of evolution, multimerization, and protein-protein interactions. Bioessays :e2200179 (2022)
Bonchuk A, Balagurov K, Georgiev P
RgGuinier 4.1 nm
Dmax 20.0 nm
VolumePorod 213 nm3

SASDP27 – BTB domain of CG6765 protein at 1.5 mg/ml

Uncharacterized protein, isoform A experimental SAS data
ALPHAFOLD model
Sample: Uncharacterized protein, isoform A hexamer, 92 kDa Drosophila melanogaster protein
Buffer: 20 mM Tris, pH 7.4, 200 mM NaCl, 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jul 8
BTB domains: A structural view of evolution, multimerization, and protein-protein interactions. Bioessays :e2200179 (2022)
Bonchuk A, Balagurov K, Georgiev P
RgGuinier 3.7 nm
Dmax 15.0 nm
VolumePorod 167 nm3

SASDPN4 – Doubly Phosphorylated p190RhoGAP Peptide Bound to p120RasGAP's SH2-SH3-SH2 Domains

Ras GTPase-activating protein 1Rho GTPase-activating protein 35 experimental SAS data
DAMMIF model
Sample: Ras GTPase-activating protein 1 monomer, 101 kDa Homo sapiens protein
Rho GTPase-activating protein 35 monomer, 3 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8 350 mM NaCl 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Dec 11
Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP. Structure (2022)
Stiegler AL, Vish KJ, Boggon TJ
RgGuinier 2.4 nm
Dmax 7.9 nm
VolumePorod 41 nm3

SASDLQ6 – High mannose glycan contactin 1 immunoglobulin domains 1-6, 2.7 μM

Contactin-1 I433V experimental SAS data
CUSTOM IN-HOUSE model
Sample: Contactin-1 I433V dimer, 134 kDa Mus musculus protein
Buffer: 25 mM HEPES, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Dec 16
Structural insights into the contactin 1 – neurofascin 155 adhesion complex Nature Communications 13(1) (2022)
Chataigner L, Gogou C, den Boer M, Frias C, Thies-Weesie D, Granneman J, Heck A, Meijer D, Janssen B
RgGuinier 4.9 nm
Dmax 14.5 nm
VolumePorod 100 nm3

SASDLY6 – High mannose glycan contactin 1 ectodomain, 2.4 μM

Contactin-1 I433V experimental SAS data
CUSTOM IN-HOUSE model
Sample: Contactin-1 I433V dimer, 220 kDa Mus musculus protein
Buffer: 25 mM HEPES, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Dec 16
Structural insights into the contactin 1 – neurofascin 155 adhesion complex Nature Communications 13(1) (2022)
Chataigner L, Gogou C, den Boer M, Frias C, Thies-Weesie D, Granneman J, Heck A, Meijer D, Janssen B
RgGuinier 6.8 nm
Dmax 19.5 nm
VolumePorod 254 nm3

SASDPF3 – Receptor-type tyrosine-protein phosphatase kappa extracellular domains (PTPRK-ECDs)

Receptor-type tyrosine-protein phosphatase kappa experimental SAS data
DAMMIN model
Sample: Receptor-type tyrosine-protein phosphatase kappa monomer, 82 kDa Homo sapiens protein
Buffer: 50 mM MES, 250 mM NaCl, 3% v/v glycerol,, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Dec 13
Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains Journal of Biological Chemistry :102750 (2022)
Hay I, Shamin M, Caroe E, Mohammed A, Svergun D, Jeffries C, Graham S, Sharpe H, Deane J
RgGuinier 7.0 nm
Dmax 26.0 nm
VolumePorod 252 nm3