Search

  
Advanced search  

151 hits found for Konarev

SASDAU5 – ad11 Fab + NGF

aD11 FabNGF experimental SAS data
DAMMIN model
Sample: aD11 Fab dimer, 50 kDa Mus musculus protein
NGF dimer, 50 kDa Mus musculus protein
Buffer: 30 mM Na-phosphate 75 mM NaCl, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 Dec 20
Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody. J Mol Biol 381(4):881-96 (2008)
...Konarev PV, Gonfloni S, Rudolph R, Svergun DI, Lamba D, Cattaneo A
RgGuinier 4.3 nm
Dmax 16.0 nm
VolumePorod 255 nm3

SASDLU5 – Complex formed between the replication origin-binding protein UL9 (C-terminal domains) with 15-bp DNA

Replication origin-binding protein15-bp DNA experimental SAS data
MONSA model
Sample: Replication origin-binding protein dimer, 81 kDa Human herpesvirus 1 … protein
15-bp DNA monomer, 9 kDa DNA
Buffer: 20 mM Tris-HCl, 50 mM NaCl, 5 mM MgCl2, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2006 May 27
Structural and biophysical characterization of the proteins interacting with the herpes simplex virus 1 origin of replication. J Biol Chem 284(24):16343-16353 (2009)
...Konarev P, Makhov AM, Fullerton SW, Sinz A, Kalkhof S, McGeehan JE, Cary PD, Griffith JD, Svergun D, Kneale GG, Tucker PA
RgGuinier 3.6 nm
Dmax 15.0 nm

SASDAV5 – apo XMRV RT

apo XMRV RT experimental SAS data
CRYSOL model
Sample: apo XMRV RT monomer, 75 kDa Escherichia coli protein
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
...Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 160 nm3

SASDLV5 – Myosin Filament-Linking Protein Myomesin-1 (domains My9-My13, dimer)

Myomesin-1 experimental SAS data
DAMMIN model
Sample: Myomesin-1 dimer, 121 kDa Homo sapiens protein
Buffer: 25 mMTris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 May 10
Superhelical architecture of the myosin filament-linking protein myomesin with unusual elastic properties. PLoS Biol 10(2):e1001261 (2012)
...Konarev PV, Svergun DI, Morris E, Rief M, Wilmanns M
RgGuinier 9.6 nm
Dmax 37.0 nm

SASDAW5 – XMRV RT + DNA/RNA hybrid

apo XMRV RTRNA_DNA hybrid substrate experimental SAS data
CRYSOL model
Sample: apo XMRV RT monomer, 75 kDa Escherichia coli protein
RNA_DNA hybrid substrate monomer, 15 kDa
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
...Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 3.5 nm
Dmax 11.5 nm
VolumePorod 155 nm3

SASDLW5 – Cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens

Cytochrome c-552 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Cytochrome c-552 hexamer, 356 kDa Thioalkalivibrio nitratireducens (strain … protein
Buffer: Tris-borate buffer, pH: 8.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 May 8
Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Biochemistry (Mosc) 73(2):164-70 (2008)
...Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG, Zvyagilskaya RA, Popov VO
RgGuinier 4.8 nm

SASDLY5 – Monomer-dimer equilibrium of glutamyl-tRNA synthetase

Glutamate--tRNA ligase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Glutamate--tRNA ligase dimer, 108 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 35 mM HEPES⁄NaOH, pH: 6.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2007 Feb 19
Kinetic and mechanistic characterization of Mycobacterium tuberculosis glutamyl-tRNA synthetase and determination of its oligomeric structure in solution FEBS Journal 276(5):1398-1417 (2009)
...Konarev P, Petoukhov M, Bernier S, Chênevert R, Svergun D, Curti B, Vanoni M
RgGuinier 3.5 nm
Dmax 11.0 nm
VolumePorod 123 nm3

SASDAV6 – Cysteine desulfurase IscS dimer

Cysteine desulfurase IscS experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Cysteine desulfurase IscS dimer, 87 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 3.2 nm
Dmax 10.9 nm

SASDAW6 – Iron-sulfur cluster assembly scaffold IscU monomer

Iron-sulfur cluster assembly scaffold protein IscU experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Iron-sulfur cluster assembly scaffold protein IscU monomer, 14 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 1.9 nm
Dmax 6.4 nm

SASDAX6 – Protein CyaY monomer

Protein CyaY experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Protein CyaY monomer, 12 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 1.5 nm
Dmax 5.0 nm

SASDAY6 – IcsS-dimer and IscU-dimer complex

Cysteine desulfurase IscSIron-sulfur cluster assembly scaffold protein IscU experimental SAS data
DAMMIF model
Sample: Cysteine desulfurase IscS dimer, 87 kDa Escherichia coli protein
Iron-sulfur cluster assembly scaffold protein IscU dimer, 29 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 3.6 nm
Dmax 12.1 nm

SASDAZ6 – CyaY-dimer and IscS-dimer complex

Cysteine desulfurase IscSProtein CyaY experimental SAS data
SASREF model
Sample: Cysteine desulfurase IscS dimer, 87 kDa Escherichia coli protein
Protein CyaY dimer, 24 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl, 50 mM NaCl, 10 mM β-mercaptoethanol and ferrous ammonium sulphate, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 3.1 nm
Dmax 10.9 nm

SASDA27 – IcsS, IscU and CyaY dimeric complex

Cysteine desulfurase IscSIron-sulfur cluster assembly scaffold protein IscUProtein CyaY experimental SAS data
SASREF model
Sample: Cysteine desulfurase IscS dimer, 87 kDa Escherichia coli protein
Iron-sulfur cluster assembly scaffold protein IscU dimer, 29 kDa Escherichia coli protein
Protein CyaY dimer, 24 kDa Escherichia coli protein
Buffer: 20 mM Tris-HCl 150 mM NaCl 10 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Nov 5
Structural bases for the interaction of frataxin with the central components of iron-sulphur cluster assembly. Nat Commun 1:95 (2010)
...Konarev PV, Iannuzzi C, Pastore C, Adinolfi S, Martin SR, Svergun DI, Pastore A
RgGuinier 3.5 nm
Dmax 11.9 nm

SASDL27 – N-Oct-3 POU transcription factor domain in complex with rat CRH DNA

POU domain, class 3, transcription factor 2Rat CRH DNA experimental SAS data
CUSTOM IN-HOUSE model
Sample: POU domain, class 3, transcription factor 2 monomer, 19 kDa Homo sapiens protein
Rat CRH DNA monomer, 15 kDa Rattus norvegicus DNA
Buffer: 50 mM Tris, 0.4 M NaCl, 2% glycerol, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2003 Oct 9
Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets Nucleic Acids Research 35(13):4420-4432 (2007)
...Konarev P, Petoukhov M, Svergun D, Erard M
RgGuinier 2.9 nm
Dmax 11.0 nm
VolumePorod 41 nm3

SASDL37 – N-Oct-3 POU transcription factor domain in complex with human DR-alpha DNA

POU domain, class 3, transcription factor 2Human DR-alpha DNA experimental SAS data
CUSTOM IN-HOUSE model
Sample: POU domain, class 3, transcription factor 2 monomer, 19 kDa Homo sapiens protein
Human DR-alpha DNA monomer, 15 kDa Homo sapiens DNA
Buffer: 50 mM Tris, 0.4 M NaCl, 2% glycerol, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2004 May 26
Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets Nucleic Acids Research 35(13):4420-4432 (2007)
...Konarev P, Petoukhov M, Svergun D, Erard M
RgGuinier 2.9 nm
Dmax 11.0 nm
VolumePorod 44 nm3

SASDJ47 – Polyglutamine protein ataxin-3 (Q13)

Ataxin-3 (polyglutamine protein ataxin-3 (Q13)) experimental SAS data
Polyglutamine protein ataxin-3 (Q13) Rg histogram
Sample: Ataxin-3 (polyglutamine protein ataxin-3 (Q13)) monomer, 41 kDa Homo sapiens protein
Buffer: 20 mM sodium phosphate buffer, 2 mM TCEP, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 May 24
Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3. Structure (2020)
...Konarev PV, Svergun DI, Pastore A
RgGuinier 4.0 nm
Dmax 14.1 nm
VolumePorod 79 nm3

SASDL47 – Oligomeric composition of AXH Domain of Ataxin-1 (wild type and A567G, I580A mutants)

Ataxin-1 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ataxin-1 monomer, 14 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Oct 21
Self-assembly and conformational heterogeneity of the AXH domain of ataxin-1: an unusual example of a chameleon fold. Biophys J 104(6):1304-13 (2013)
...Konarev PV, Svergun DI, Martin SR, Chen YW, Pastore A
RgGuinier 5.5 nm

SASDJ57 – Polyglutamine protein ataxin-3 (Q54)

Ataxin-3 (polyglutamine protein ataxin-3 (Q54)) experimental SAS data
Polyglutamine protein ataxin-3 (Q54) Rg histogram
Sample: Ataxin-3 (polyglutamine protein ataxin-3 (Q54)) monomer, 46 kDa protein
Buffer: 20 mM sodium phosphate buffer, 2 mM TCEP, 5% glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 May 24
Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3. Structure (2020)
...Konarev PV, Svergun DI, Pastore A
RgGuinier 4.2 nm
Dmax 15.5 nm
VolumePorod 89 nm3

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)
...Konarev PV, Svergun DI, Merli A, Závodszky P, Weiss MS, Vas M
RgGuinier 2.8 nm

SASDL67 – Mutation of the Active Site Residues of 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 2012 Nov 16
Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure. Biochemistry 55(3):560-74 (2016)
...Konarev PV, Lábas A, Oláh J, Palló A, Svergun DI, Merli A, Závodszky P, Weiss MS, Vas M
RgGuinier 2.8 nm

SASDM77 – Full-length polypyrimidine tract binding protein (PTB)

Polypyrimidine tract-binding protein 2 experimental SAS data
DAMMIN model
Sample: Polypyrimidine tract-binding protein 2 monomer, 57 kDa Homo sapiens protein
Buffer: 25 mM Tris, 250 mM NaCl, 2 mM DTT, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2004 Feb 11
Structure and RNA interactions of the N-terminal RRM domains of PTB. Structure 12(9):1631-43 (2004)
...Konarev PV, Curry S, Matthews S
RgGuinier 4.0 nm
Dmax 14.0 nm
VolumePorod 117 nm3

SASDM87 – Mouse ProNGF - pro-form of the NGF (nerve growth factor)

Mouse ProNGF - pro-form of the NGF (nerve growth factor) experimental SAS data
DAMMIN model
Sample: Mouse ProNGF - pro-form of the NGF (nerve growth factor) dimer, 100 kDa Mus musculus protein
Buffer: 50 mM Na-phosphate, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 Jul 18
Structural and functional properties of mouse proNGF. Biochem Soc Trans 34(Pt 4):605-6 (2006)
...Konarev PV, Covaceuszach S, Schwarz E, Cattaneo A, Lamba D, Svergun DI
RgGuinier 3.0 nm
Dmax 11.0 nm
VolumePorod 97 nm3

SASDM97 – Recombinant monoclonal anti-proNGF antibody in single chain Fv fragment (scFv)

Recombinant monoclonal anti-proNGF antibody in single chain Fv fragment (scFv) experimental SAS data
BUNCH model
Sample: Recombinant monoclonal anti-proNGF antibody in single chain Fv fragment (scFv) monomer, 29 kDa protein
Buffer: phosphate buffered saline, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 Oct 21
Direct intracellular selection and biochemical characterization of a recombinant anti-proNGF single chain antibody fragment. Arch Biochem Biophys 522(1):26-36 (2012)
...Konarev PV, Visintin M, Scardigli R, Fasulo L, Lamba D, Svergun DI, Cattaneo A
RgGuinier 2.7 nm
Dmax 8.0 nm
VolumePorod 39 nm3

SASDMA7 – Prion protein aggregate in solution

Major prion protein experimental SAS data
DAMMIN model
Sample: Major prion protein 24-mer, 664 kDa Homo sapiens protein
Buffer: 5 mM sodium acetate, pH: 5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 Jun 2
Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. J Struct Biol 157(2):308-20 (2007)
...Konarev PV, Svergun DI, Fittschen UE, Broekaert JA, Bruns O, Georgieva D, Mandelkow E, Genov N, Betzel C
RgGuinier 9.8 nm
Dmax 32.0 nm
VolumePorod 3320 nm3

SASDMC7 – Nuclear fragile X mental retardation-interacting protein 2 (FRMP)

Nuclear fragile X mental retardation-interacting protein 2 experimental SAS data
DAMMIN model
Sample: Nuclear fragile X mental retardation-interacting protein 2 monomer, 59 kDa Homo sapiens protein
Buffer: 50 mM Tris-HCl pH 8.0, 5 mM TCEP, pH:
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2007 Oct 11
A study of the ultrastructure of fragile-X-related proteins. Biochem J 419(2):347-57 (2009)
...Konarev PV, Eccleston J, Taylor IA, Svergun DI, Pastore A
RgGuinier 4.1 nm
Dmax 15.0 nm
VolumePorod 92 nm3

SASDHN7 – Emfourin (M4in) from Serratia proteamaculans, M4 family peptidase inhibitor

Emfourin (Protealysin-associated protein) experimental SAS data
DAMFILT model
Sample: Emfourin (Protealysin-associated protein) monomer, 13 kDa Serratia proteamaculans protein
Buffer: 50 mM Tris-HCL, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Apr 22
NMR structure of emfourin, a novel protein metalloprotease inhibitor: insights into the mechanism of action. J Biol Chem :104585 (2023)
...Konarev P, Varizhuk A, Lesovoy D, Arseniev A, Kostrov S, Bocharov E, Demidyuk I
RgGuinier 1.7 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDLR7 – The HC Fragment of Tetanus Toxin

Hc fragment of Tetanus toxin experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Hc fragment of Tetanus toxin dimer, 103 kDa Clostridium tetani (strain … protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, pH: 7.8
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2004 May 14
The HC fragment of tetanus toxin forms stable, concentration-dependent dimers via an intermolecular disulphide bond. J Mol Biol 365(1):123-34 (2007)
...Konarev PV, Yao ZP, Robinson CV, Brown KA, Fairweather N
RgGuinier 4.0 nm
Dmax 13.2 nm
VolumePorod 150 nm3

SASDMX8 – Iron oxide nanoparticles (NP-N2) (30% of 9 kDa PEG tails)

Iron oxide nanoparticles (NP-N2) (30% of 9 kDa PEG tails) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-N2) (30% of 9 kDa PEG tails) 0, 5000 kDa
Buffer: 0.05 M Tris-HCl, 0.05 M NaCl, 0.01 M KCl, 0.005 M MgCl2, pH: 4.6
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 25.0 nm

SASDMY8 – Iron oxide nanoparticles (NP-N3) (60% of 9 kDa PEG tails)

Iron oxide nanoparticles (NP-N3) (60% of 9 kDa PEG tails) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-N3) (60% of 9 kDa PEG tails) 0, 5000 kDa
Buffer: 0.05 M Tris-HCl, 0.05 M NaCl, 0.01 M KCl, 0.005 M MgCl2, pH: 4.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 26.0 nm

SASDMZ8 – Iron oxide nanoparticles (NP-P3) (60% of 5 kDa PEG tails)

Iron oxide nanoparticles (NP-P3) (60% of 5 kDa PEG tails) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-P3) (60% of 5 kDa PEG tails) 0, 5000 kDa
Buffer: 0.05 M Tris-HCl, 0.05 M NaCl, 0.01 M KCl, 0.005 M MgCl2, pH: 4.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 26.0 nm

SASDM29 – Iron oxide nanoparticles (NP-N2) encapsulated into brome mosaic virus (BMV)

Iron oxide nanoparticles (NP-N2) encapsulated into brome mosaic virus (BMV) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-N2) encapsulated into brome mosaic virus (BMV) 0, 5000 kDa
Buffer: 0.05 M Tris-HCl, 0.05 M NaCl, 0.01 M KCl, 0.005 M MgCl2, pH: 4.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 25.5 nm

SASDM39 – Iron oxide nanoparticles (NP-P3) encapsulated into brome mosaic virus (BMV)

Iron oxide nanoparticles (NP-P3) encapsulated into brome mosaic virus (BMV) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-P3) encapsulated into brome mosaic virus (BMV) 0, 5000 kDa
Buffer: 50 mM Tris-HCl, 50 mM NaCl, 10 mM KCl, 5 mM MgCl2, pH: 4.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 25.0 nm

SASDM49 – Iron oxide nanoparticles (NP-N3) encapsulated into hepatitis B virus (HBV)

Iron oxide nanoparticles (NP-N3) encapsulated into hepatitis B virus (HBV) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Iron oxide nanoparticles (NP-N3) encapsulated into hepatitis B virus (HBV) 0, 5000 kDa
Buffer: 0.5 M LiCl, 50 mM HEPES, 2 mM DTT, pH 7.5, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 25.5 nm

SASDM59 – brome mosaic virus (BMV)

brome mosaic virus (BMV) experimental SAS data
brome mosaic virus (BMV) Kratky plot
Sample: brome mosaic virus (BMV) monomer, 5000 kDa
Buffer: 50 mM Tris-HCl, 50 mM NaCl, 10 mM KCl, 5 mM MgCl2, pH: 4.6
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 31.7 nm

SASDM69 – Hepatitis B virus (HBV)

Hepatitis B virus (HBV) experimental SAS data
Hepatitis B virus (HBV) Kratky plot
Sample: Hepatitis B virus (HBV) None,
Buffer: 0.5 M LiCl, 50 mM HEPES, 2 mM DTT, pH 7.5, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 23
Coat Protein-Dependent Behavior of Poly(ethylene glycol) Tails in Iron Oxide Core Virus-like Nanoparticles. ACS Appl Mater Interfaces 7(22):12089-98 (2015)
...Konarev PV, Svergun DI, Dragnea B, Bronstein LM
Dmax 32.0 nm

SASDM79 – Lysozyme crystallization solutions with precipitants from crystallization kits CS 1 and CS2 (mixture of monomers, dimers and octamers, with octamer volume fractions from 0 to 0.7%)

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 100 mM HEPES pH 7.5, 20 %(v/v) jeffamine M-600, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Aug 28
The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase. Acta Naturae 15(1):58-68 (2023)
...Konarev PV, Pisarevsky YV, Dyakova YA, Kovalchuk MV
RgGuinier 1.8 nm

SASDM89 – Lysozyme crystallization solutions with precipitants from crystallization kits CS 1 and CS2 (mixture of monomers, dimers and octamers, with octamer volume fractions from 0.9% to 4.4%)

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 100 mM sodium acetate, pH 4.6, 2.0 M sodium formate, pH: 4.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Aug 28
The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase. Acta Naturae 15(1):58-68 (2023)
...Konarev PV, Pisarevsky YV, Dyakova YA, Kovalchuk MV
RgGuinier 2.2 nm

SASDM99 – Lysozyme crystallization solutions with precipitants from crystallization kits CS 1 and CS2 (mixture of monomers, dimers and octamers, with octamer volume fractions from 4.9% to 21.1%)

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 200 mM K/Na tartrate, 100 mM tri-sodium citrate pH 5.6, 2.0 M ammonium sulfate, pH: 5.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Aug 28
The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase. Acta Naturae 15(1):58-68 (2023)
...Konarev PV, Pisarevsky YV, Dyakova YA, Kovalchuk MV
RgGuinier 2.4 nm

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)
...Konarev P, Graewert M, 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)
...Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 165 nm3

SASDEX9 – Class II pyruvate aldolase (HpcH/HpaI aldolase), wild-type hexamer in HEPES isolated using SEC-SAXS

HpcH/HpaI aldolase experimental SAS data
GASBOR model
Sample: HpcH/HpaI aldolase hexamer, 165 kDa Rhizorhabdus wittichii RW1 protein
Buffer: 20 mM HEPES,, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 23
EFAMIX , a tool to decompose inline chromatography SAXS data from partially overlapping components Protein Science (2021)
Konarev P, Graewert M, Jeffries C, Fukuda M, Cheremnykh T, Volkov V, Svergun D
RgGuinier 3.3 nm
Dmax 9.4 nm
VolumePorod 233 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)
...Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 151 nm3

SASDPZ8 – Gli-233 - ssDNA aptamer specific to glioma brain tumor cells

Gli-233 - ssDNA aptamer to glioma brain tumor cells experimental SAS data
GROMACS model
Sample: Gli-233 - ssDNA aptamer to glioma brain tumor cells monomer, 10 kDa Artificially synthesized DNA
Buffer: Dulbecco phosphate-buffered saline (DPBS, with Ca and Mg), pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 17
Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells Molecular Therapy - Nucleic Acids (2023)
...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, Ba...
RgGuinier 1.9 nm
Dmax 6.8 nm
VolumePorod 13 nm3

SASDRN9 – Polydisperse core-shell ellipsoidal micelles of Polysorbate 20 (PS20) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml)

Polysorbate 20 (PS20) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polysorbate 20 (PS20) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) 0, 45 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 2
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.4 nm
Dmax 8.6 nm

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)
...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, Ba...
RgGuinier 2.8 nm
Dmax 11.5 nm
VolumePorod 35 nm3

SASDRQ9 – Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml)

Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) 20-mer, 24 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Mar 6
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.0 nm
Dmax 8.0 nm

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)
...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, Ba...
RgGuinier 2.8 nm
Dmax 11.5 nm
VolumePorod 34 nm3

SASDRS9 – Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml)

Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with no or low amount of the fatty acid myristic acid (MA) (< 100 µg/ml) 0, 42 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Oct 29
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.3 nm
Dmax 8.3 nm

SASDRP9 – Polydisperse core-shell ellipsoidal micelles of Polysorbate 20 (PS20) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml)

Polydisperse core-shell ellipsoidal micelles of Polysorbate 20 (PS20) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polydisperse core-shell ellipsoidal micelles of Polysorbate 20 (PS20) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) 0, 45 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 2
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.5 nm
Dmax 8.8 nm

SASDRR9 – Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml)

Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polydisperse core-shell ellipsoidal micelles of POE sorbitan monolaurate fraction (F2) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) 22-mer, 26 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Mar 6
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.1 nm
Dmax 8.3 nm

SASDRT9 – Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml)

Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Polydisperse core-shell ellipsoidal micelles of POE sorbitan higher order esters fraction (F4) with high amount of the fatty acid myristic acid (MA) (> 500 µg/ml) 0, 42 kDa
Buffer: aqueous solution of 4% methanol, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Oct 29
Small-angle x-ray scattering investigation of the integration of free fatty acids in polysorbate 20 micelles Biophysical Journal (2023)
...Konarev P, Svergun D, Nagel N
RgGuinier 3.5 nm
Dmax 8.7 nm