Browse by MODEL: Ab initio only

SASDTZ4 – I-actin - Skeletal muscle actin from Oryctolagus cuniculus: oligomer of time-inactivated actin (peak SEC fraction)

Actin, alpha skeletal muscle experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Actin, alpha skeletal muscle monomer, 42 kDa Oryctolagus cuniculus protein
Buffer: 5 mM Tris/Tris-HCl, 2.0 mM EDTA, pH: 8.1
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2021 Nov 16
Small-angle X-ray scattering structural insights into alternative pathway of actin oligomerization associated with inactivated state Biochemical and Biophysical Research Communications :149340 (2023)
Ryzhykau Y, Povarova O, Dronova E, Kuklina D, Antifeeva I, Ilyinsky N, Okhrimenko I, Semenov Y, Kuklin A, Ivanovich V, Fonin A, Uversky V, Turoverov K, Kuznetsova I
RgGuinier 4.9 nm
Dmax 22.0 nm
VolumePorod 549 nm3

SASDT25 – G- / I-actin mixture - Skeletal muscle actin from Oryctolagus cuniculus: mixture of globular actin monomers and inactivated actin monomers and dimers

Actin, alpha skeletal muscle experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Actin, alpha skeletal muscle monomer, 42 kDa Oryctolagus cuniculus protein
Buffer: 5 mM Tris, 0.1 mM CaCl2, 1 mM NaN3, 0.2 mM ATP, pH: 8.1
Experiment: SAXS data collected at Rigaku MicroMax 007-HF, Moscow Institute of Physics and Technology (MIPT) on 2021 Jul 5
Small-angle X-ray scattering structural insights into alternative pathway of actin oligomerization associated with inactivated state Biochemical and Biophysical Research Communications :149340 (2023)
Ryzhykau Y, Povarova O, Dronova E, Kuklina D, Antifeeva I, Ilyinsky N, Okhrimenko I, Semenov Y, Kuklin A, Ivanovich V, Fonin A, Uversky V, Turoverov K, Kuznetsova I
RgGuinier 3.1 nm
Dmax 12.0 nm
VolumePorod 84 nm3

SASDLC7 – Polyribonucleotide nucleotidyltransferase (PNPase): apo form

Polyribonucleotide nucleotidyltransferase experimental SAS data
DAMFILT model
Sample: Polyribonucleotide nucleotidyltransferase trimer, 246 kDa Campylobacter jejuni subsp. … protein
Buffer: 20 mM Tris-HCl, 10 mM NAH2PO4, 60 mM KCl, 1 mM MgCl2, 2 mM DTT, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Mar 17
Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie (2023)
Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG
RgGuinier 3.9 nm
Dmax 11.0 nm
VolumePorod 310 nm3

SASDLD7 – Polyribonucleotide nucleotidyltransferase (PNPase): 2-AMP complex

Polyribonucleotide nucleotidyltransferase experimental SAS data
DAMFILT model
Sample: Polyribonucleotide nucleotidyltransferase trimer, 237 kDa Campylobacter jejuni subsp. … protein
Buffer: 20 mM Tris.HCl, 10 mM NAH2PO4, 60 mM KCl, 1 mM MgCl2, 2 mM DTT, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Mar 17
Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie (2023)
Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG
RgGuinier 3.9 nm
Dmax 11.0 nm
VolumePorod 315 nm3

SASDLE7 – Polyribonucleotide nucleotidyltransferase (PNPase): 2-GMP complex

Polyribonucleotide nucleotidyltransferase experimental SAS data
DAMFILT model
Sample: Polyribonucleotide nucleotidyltransferase trimer, 237 kDa Campylobacter jejuni subsp. … protein
Buffer: 20 mM Tris.HCl, 10 mM NAH2PO4, 60 mM KCl, 1mM MgCl2, 2 mM DTT, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Mar 17
Structure and function of Campylobacter jejuni polynucleotide phosphorylase (PNPase): Insights into the role of this RNase in pathogenicity. Biochimie (2023)
Bárria C, Athayde D, Hernandez G, Fonseca L, Casinhas J, Cordeiro TN, Archer M, Arraiano CM, Brito JA, Matos RG
RgGuinier 3.9 nm
Dmax 11.0 nm
VolumePorod 312 nm3

SASDR96 – Human DjC20/DnaJC20/HscB iron-sulfur cluster co-chaperone protein

Iron-sulfur cluster co-chaperone protein HscB experimental SAS data
DAMMIF model
Sample: Iron-sulfur cluster co-chaperone protein HscB monomer, 25 kDa Homo sapiens protein
Buffer: 25 mM Tris-HCl, 50 mM NaCl, 5 mM KCl, 2 mM β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at SAXS1 Beamline, Brazilian Synchrotron Light Laboratory on 2018 Aug 14
Structural characterization of the human DjC20/HscB cochaperone in solution Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics :140970 (2023)
de Souza Coto A, Pereira A, Oliveira S, de Oliveira Moritz M, da Rocha A, Dores-Silva P, da Silva N, de Araújo Nogueira A, Gava L, Seraphim T, Borges J
RgGuinier 2.5 nm
Dmax 9.0 nm
VolumePorod 40 nm3

SASDSH7 – Cationic liposomes containing DOTMA:DOPE (2:1) with negatively charged messenger RNA (mRNA) (raito 0.65:1)

mRNA -- proprietary sequence(R)-N,N,N-trimethyl-2-3-dioleyloxy-1-propanaminium chloride1,2-dioleoyl-sn-glycero-3-phosphoethanolamine experimental SAS data
OTHER [STATIC IMAGE] model
Sample: MRNA -- proprietary sequence, 400 kDa RNA
(R)-N,N,N-trimethyl-2-3-dioleyloxy-1-propanaminium chloride, 1 kDa lipid
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, 1 kDa lipid
Buffer: 10 mM HEPES, 5 mM NaCl, 0.1 mM EDTA, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Jun 9
Quantitative size-resolved characterization of mRNA nanoparticles by in-line coupling of asymmetrical-flow field-flow fractionation with small angle X-ray scattering. Sci Rep 13(1):15764 (2023)
Graewert MA, Wilhelmy C, Bacic T, Schumacher J, Blanchet C, Meier F, Drexel R, Welz R, Kolb B, Bartels K, Nawroth T, Klein T, Svergun D, Langguth P, Haas H

SASDRJ8 – A de novo enzyme, ferric enterobactin esterase Syn-F4

De novo enterobactin esterase Syn-F4 (K4T) experimental SAS data
DAMMIN model
Sample: De novo enterobactin esterase Syn-F4 (K4T) dimer, 25 kDa synthetic construct protein
Buffer: 25 mM MES, 100 mM NaCl, 10% glycerol, 200 mM Arg-HCl, pH: 6.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 Feb 11
Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4. Proc Natl Acad Sci U S A 120(38):e2218281120 (2023)
Kurihara K, Umezawa K, Donnelly AE, Sperling B, Liao G, Hecht MH, Arai R
RgGuinier 2.5 nm
Dmax 10.0 nm
VolumePorod 40 nm3

SASDS32 – Reconstituted sulfite reductase crosslinked dodecamer with partially deuterated hemoprotein in 86% D2O

Sulfite reductase [NADPH] hemoprotein beta-componentSulfite reductase [NADPH] flavoprotein alpha-component (E121C, C162T, C552S, N556C) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component tetramer, 256 kDa Escherichia coli (strain … protein
Sulfite reductase [NADPH] flavoprotein alpha-component (E121C, C162T, C552S, N556C) octamer, 566 kDa Escherichia coli (strain … protein
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS, Spallation Neutron Source on 2023 Apr 24
Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase. J Struct Biol 215(4):108028 (2023)
Walia N, Murray DT, Garg Y, He H, Weiss KL, Nagy G, Elizabeth Stroupe M
RgGuinier 7.5 nm
Dmax 22.6 nm
VolumePorod 823 nm3

SASDS42 – Reconstituted sulfite reductase crosslinked dodecamer with partially deuterated hemoprotein in 41% D2O

Sulfite reductase [NADPH] hemoprotein beta-componentSulfite reductase [NADPH] flavoprotein alpha-component (E121C, C162T, C552S, N556C) experimental SAS data
Sample: Sulfite reductase [NADPH] hemoprotein beta-component tetramer, 256 kDa Escherichia coli (strain … protein
Sulfite reductase [NADPH] flavoprotein alpha-component (E121C, C162T, C552S, N556C) octamer, 566 kDa Escherichia coli (strain … protein
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 1 mM EDTA, pH: 7.8
Experiment: SANS data collected at EQ-SANS, Spallation Neutron Source on 2022 Aug 24
Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase. J Struct Biol 215(4):108028 (2023)
Walia N, Murray DT, Garg Y, He H, Weiss KL, Nagy G, Elizabeth Stroupe M
RgGuinier 11.1 nm
Dmax 32.4 nm
VolumePorod 138 nm3