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23 hits found for Dadinova

SASDKN2 – Matrix protein from Newcastle disease virus at neutral pH

Matrix protein experimental SAS data
DAMMIN model
Sample: Matrix protein , 40 kDa Newcastle disease virus … protein
Buffer: STE buffer 100 mM NaCl, 10 mM Tris-HCl, and 1 mM EDTA, pH: 4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 11
Solution Structure, Self-Assembly, and Membrane Interactions of the Matrix Protein from Newcastle Disease Virus at Neutral and Acidic pH Journal of Virology 93(6) (2019)
...Dadinova L, Fedorova N, Tashkin V, Timofeeva T, Ksenofontov A, Loshkarev N, Baratova L, Jeffries C, Svergun D, Batishchev O, García-Sastre A
RgGuinier 3.5 nm

SASDKP2 – Matrix protein from Newcastle disease virus at acidic pH

Matrix protein experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Matrix protein dimer, 79 kDa Newcastle disease virus … protein
Buffer: STE buffer 100 mM NaCl, 10 mM Tris-HCl, and 1 mM EDTA, pH: 4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Dec 11
Solution Structure, Self-Assembly, and Membrane Interactions of the Matrix Protein from Newcastle Disease Virus at Neutral and Acidic pH Journal of Virology 93(6) (2019)
...Dadinova L, Fedorova N, Tashkin V, Timofeeva T, Ksenofontov A, Loshkarev N, Baratova L, Jeffries C, Svergun D, Batishchev O, García-Sastre A
RgGuinier 3.3 nm

SASDBY2 – Inorganic pyrophosphatase (PPase) from E. coli

Inorganic pyrophosphatase (PPase) from E. coli experimental SAS data
DAMMIN model
Sample: Inorganic pyrophosphatase (PPase) from E. coli hexamer, 117 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 30
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
RgGuinier 3.0 nm
Dmax 9.0 nm
VolumePorod 166 nm3

SASDBZ2 – Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli experimental SAS data
DAMMIN model
Sample: Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli decamer, 381 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 30
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
RgGuinier 4.4 nm
Dmax 12.7 nm
VolumePorod 484 nm3

SASDB23 – 5-keto-4-deoxyuronate isomerase (KduI) from E. coli

5-keto-4-deoxyuronate isomerase (KduI) from E. coli experimental SAS data
NONE model
Sample: 5-keto-4-deoxyuronate isomerase (KduI) from E. coli None, Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 20
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
RgGuinier 4.5 nm

SASDB33 – Glutamate decarboxylase alpha (GadA) from E. coli

Glutamate decarboxylase alpha (GadA) from E. coli experimental SAS data
SASREF MX model
Sample: Glutamate decarboxylase alpha (GadA) from E. coli monomer, 53 kDa Escherichia coli protein
Buffer: 50 mM Tris 10 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Jun 20
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
RgGuinier 4.8 nm
VolumePorod 410 nm3

SASDDF3 – Macrophage migration inhibitory factor bound to Ceruloplasmin (MIF-CP complex)

Macrophage migration inhibitory factorCeruloplasmin experimental SAS data
CLUSPRO model
Sample: Macrophage migration inhibitory factor trimer, 37 kDa Homo sapiens protein
Ceruloplasmin monomer, 122 kDa Homo sapiens protein
Buffer: 50mkm CuSO4, 100mM Hepes, pH: 7.4
Experiment: SAXS data collected at HECUS System-3, None on 2015 Dec 22
Structural Study of the Complex Formed by Ceruloplasmin and Macrophage Migration Inhibitory Factor. Biochemistry (Mosc) 83(6):701-707 (2018)
...Dadinova LA, Petoukhov MV, Bourenkov G, Dubova KM, Amarantov SV, Volkov VV, Kostevich VA, Gorbunov NP, Grudinina NA, Vasilyev VB, Samygina VR
RgGuinier 3.6 nm
Dmax 14.4 nm
VolumePorod 228 nm3

SASDKS3 – The dimeric ectodomain of the alkali-sensing insulin receptor–related receptor (ectoIRR) at pH7

Insulin receptor-related protein experimental SAS data
CORAL model
Sample: Insulin receptor-related protein dimer, 201 kDa Homo sapiens protein
Buffer: 150 mM NaCl, 20 mM Tris, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Oct 22
The dimeric ectodomain of the alkali-sensing insulin receptor-related receptor (ectoIRR) has a droplike shape. J Biol Chem 294(47):17790-17798 (2019)
...Dadinova LA, Loshkarev NA, Goryashchenko AS, Bocharov EV, Jeffries CM, Svergun DI, Batishchev OV, Petrenko AG
RgGuinier 5.4 nm
Dmax 19.5 nm
VolumePorod 444 nm3

SASDKT3 – The dimeric ectodomain of the alkali-sensing insulin receptor–related receptor (ectoIRR) at pH9

Insulin receptor-related protein experimental SAS data
CORAL model
Sample: Insulin receptor-related protein dimer, 201 kDa Homo sapiens protein
Buffer: 150 mM NaCl, 20 mM Tris, pH: 9
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Oct 22
The dimeric ectodomain of the alkali-sensing insulin receptor-related receptor (ectoIRR) has a droplike shape. J Biol Chem 294(47):17790-17798 (2019)
...Dadinova LA, Loshkarev NA, Goryashchenko AS, Bocharov EV, Jeffries CM, Svergun DI, Batishchev OV, Petrenko AG
RgGuinier 5.3 nm
Dmax 19.0 nm
VolumePorod 430 nm3

SASDKD4 – In vitro DNA protection during starvation protein (Dps)/DNA co-crystallization

DNA protection during starvation protein experimental SAS data
DNA protection during starvation protein Kratky plot
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM Tris-HCl, 50 mM NaCl, 0.5 mM EDTA, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 27
Protective Dps-DNA co-crystallization in stressed cells: an in vitro structural study by small-angle X-ray scattering and cryo-electron tomography. FEBS Lett 593(12):1360-1371 (2019)
Dadinova LA, Chesnokov YM, Kamyshinsky RA, Orlov IA, Petoukhov MV, Mozhaev AA, Soshinskaya EY, Lazarev VN, Manuvera VA, Orekhov AS, Vasiliev AL, Shtykova EV

SASDKE4 – Polymorphic DNA protection during starvation protein (Dps)-DNA сo-сrystals

DNA protection during starvation protein experimental SAS data
DNA protection during starvation protein Kratky plot
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 10 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 28
Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering. Biomolecules 10(1) (2019)
...Dadinova L, Mozhaev A, Orlov I, Petoukhov M, Orekhov A, Shtykova E, Vasiliev A

SASDKF4 – DNA binding protein of starvation (DPS)

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 225 kDa Escherichia coli protein
Buffer: 50 mM Tris-HCl, 50 mM NaCl, 0.5 mM EDTA, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 26
Spatial Organization of Dps and DNA-Dps Complexes. J Mol Biol :166930 (2021)
...Dadinova LA, Petoukhov MV, Yu Soshinskaya E, Mozhaev AA, Klinov DV, Schäffer TE, Shtykova EV, Batishchev OV
RgGuinier 3.9 nm
Dmax 14.0 nm
VolumePorod 314 nm3

SASDBS4 – Glutamate decarboxylase alpha (GadA) from E. coli, low salt

Glutamate decarboxylase alpha (GadA) from E. coli experimental SAS data
SASREF MX model
Sample: Glutamate decarboxylase alpha (GadA) from E. coli monomer, 53 kDa Escherichia coli protein
Buffer: 50 mM Tris, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jul 29
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 11(5):e0156105 (2016)
Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
RgGuinier 4.4 nm
VolumePorod 450 nm3

SASDKY4 – DNA binding protein of starvation (no EDTA)

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 225 kDa Escherichia coli protein
Buffer: 20мМ Tris-HCl, 100 мМ NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 19
Spatial Organization of Dps and DNA-Dps Complexes. J Mol Biol :166930 (2021)
...Dadinova LA, Petoukhov MV, Yu Soshinskaya E, Mozhaev AA, Klinov DV, Schäffer TE, Shtykova EV, Batishchev OV
RgGuinier 3.8 nm
Dmax 11.9 nm
VolumePorod 277 nm3

SASDMF5 – Two-component synthetic liposomes composed of 10% DOPS + 90% DOPC lipid mixtures loaded with M1 protein

Two-component synthetic liposomes composed of 10% DOPS + 90% DOPC lipid mixtures loaded with M1 protein ((lipid:M1 molar ratio 20:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Two-component synthetic liposomes composed of 10% DOPS + 90% DOPC lipid mixtures loaded with M1 protein ((lipid:M1 molar ratio 20:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 30
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDMG5 – Two-component synthetic liposomes composed of 30% DOPS + 70% DOPC lipid mixtures loaded with M1 protein

Two-component synthetic liposomes composed of 30% DOPS + 70% DOPC lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Two-component synthetic liposomes composed of 30% DOPS + 70% DOPC lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 31
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDMH5 – Four-component synthetic liposomes composed of 30% bPS + 10% POPC + 40% SM + 20% Chol lipid mixtures loaded with M1 protein

Four-component synthetic liposomes composed of 30% bPS + 10% POPC + 40% SM + 20% Chol lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Four-component synthetic liposomes composed of 30% bPS + 10% POPC + 40% SM + 20% Chol lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 31
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDMJ5 – Four-component synthetic liposomes composed of 20% bPS + 13.3% POPC + 33.3% SM + 33.3% Chol lipid mixtures loaded with M1 protein

Four-component synthetic liposomes composed of 20% bPS + 13.3% POPC + 33.3% SM + 33.3% Chol lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Four-component synthetic liposomes composed of 20% bPS + 13.3% POPC + 33.3% SM + 33.3% Chol lipid mixtures loaded with M1 protein (lipid:M1 molar ration 20:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 31
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDMK5 – Native liposomes composed of lipids extracted from A/Puerto Rico/8/34 (H1N1) virus envelope loaded with M1 protein.

Native liposomes composed of lipids extracted from A/Puerto Rico/8/34 (H1N1) virus envelope loaded with M1 protein. (lipid:M1 molar ration 4:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Native liposomes composed of lipids extracted from A/Puerto Rico/8/34 (H1N1) virus envelope loaded with M1 protein. (lipid:M1 molar ration 4:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 26
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDML5 – Proteoliposomes composed of lipids from A/Puerto Rico/8/34 (H1N1) virus envelope together with the HA LI45 peptides loaded with M1 protein

Proteoliposomes composed of lipids from A/Puerto Rico/8/34 (H1N1) virus envelope together with the HA LI45 peptides loaded with M1 protein (lipid:M1 molar ration 4:1) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Proteoliposomes composed of lipids from A/Puerto Rico/8/34 (H1N1) virus envelope together with the HA LI45 peptides loaded with M1 protein (lipid:M1 molar ration 4:1) monomer, 2000 kDa
Buffer: 100 mM NaCl, 50 mM MES buffer, pH: 6.8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 26
The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer Membranes 11(10):772 (2021)
...Dadinova L, Timofeeva T, Abramchuk S, Moiseenko A, Baratova L, Svergun D, Batishchev O

SASDPX7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 50 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
...Dadinova L
RgGuinier 3.8 nm
Dmax 14.0 nm
VolumePorod 32 nm3

SASDPY7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 500 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
...Dadinova L
RgGuinier 7.4 nm
Dmax 12.0 nm

SASDPZ7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 2000 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV...

DNA protection during starvation protein experimental SAS data
DAMMIN model
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Oct 5
An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps Moscow University Physics Bulletin 77(6):858-867 (2023)
...Dadinova L
RgGuinier 7.1 nm
Dmax 14.0 nm