Browse by MODEL: Ab initio only

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

SASDS52 – Sulfite reductase crosslinked dodecamer

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 Jul 15
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 10.3 nm
Dmax 31.0 nm
VolumePorod 1170 nm3

SASDSF2 – K48-linked diubiquitin

Polyubiquitin-C experimental SAS data
OTHER model
Sample: Polyubiquitin-C monomer, 17 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Feb 1
Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin. Dalton Trans (2023)
Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D
RgGuinier 1.9 nm
Dmax 6.5 nm
VolumePorod 22 nm3

SASDSG2 – K48-linked diubiquitin in the presence of zinc ion

Polyubiquitin-C experimental SAS data
Sample: Polyubiquitin-C monomer, 17 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Feb 1
Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin. Dalton Trans (2023)
Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D
RgGuinier 2.0 nm
Dmax 7.5 nm
VolumePorod 20 nm3

SASDSH2 – K48-linked diubiquitin in the presence of copper (II) ion

Polyubiquitin-C experimental SAS data
Sample: Polyubiquitin-C monomer, 17 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, pH: 7
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Feb 1
Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin. Dalton Trans (2023)
Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D
RgGuinier 1.9 nm
Dmax 6.3 nm
VolumePorod 20 nm3

SASDMV5 – Kinesin superfamily protein 3 A/B and kinesin associated protein 3 (KAP)

Kinesin-like protein KIF3BKinesin-associated protein 3Kinesin-like protein KIF3A experimental SAS data
DAMMIF model
Sample: Kinesin-like protein KIF3B monomer, 32 kDa Mus musculus protein
Kinesin-associated protein 3 monomer, 81 kDa Mus musculus protein
Kinesin-like protein KIF3A monomer, 28 kDa Mus musculus protein
Buffer: 20 mM Tris-HCl, 200 mM NaCl, 5% glycerol, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BL-15A2, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2020 Jun 24
The two-step cargo recognition mechanism of heterotrimeric kinesin. EMBO Rep :e56864 (2023)
Jiang X, Ogawa T, Yonezawa K, Shimizu N, Ichinose S, Uchihashi T, Nagaike W, Moriya T, Adachi N, Kawasaki M, Dohmae N, Senda T, Hirokawa N
RgGuinier 5.8 nm
Dmax 27.0 nm
VolumePorod 557 nm3

SASDMW5 – Kinesin superfamily protein 3 A/B and kinesin associated protein 3 (KAP) with APC ARM

Adenomatous polyposis coli protein (N-terminal ARM domain)Kinesin-like protein KIF3AKinesin-like protein KIF3BKinesin-associated protein 3 experimental SAS data
DAMMIF model
Sample: Adenomatous polyposis coli protein (N-terminal ARM domain) monomer, 75 kDa Mus musculus protein
Kinesin-like protein KIF3A monomer, 28 kDa Mus musculus protein
Kinesin-like protein KIF3B monomer, 32 kDa Mus musculus protein
Kinesin-associated protein 3 monomer, 81 kDa Mus musculus protein
Buffer: 25 mM Tris-HCl, 200 mM NaCl, 1 mM DTT, 5% glycerol, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2020 Nov 17
The two-step cargo recognition mechanism of heterotrimeric kinesin. EMBO Rep :e56864 (2023)
Jiang X, Ogawa T, Yonezawa K, Shimizu N, Ichinose S, Uchihashi T, Nagaike W, Moriya T, Adachi N, Kawasaki M, Dohmae N, Senda T, Hirokawa N
RgGuinier 5.4 nm
Dmax 19.5 nm
VolumePorod 763 nm3