Browse by MODEL: Ab initio only

SASDQG7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl)

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.9 nm
Dmax 20.7 nm
VolumePorod 206 nm3

SASDQH7 – Thermoanearobacter tengcongensis (Tte) fecB RNA riboswitch aptamer domain (rCbl) in the presence of coenzyme B12

Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain experimental SAS data
OTHER model
Sample: Thermoanearobacter tengcongensis (Tte) fecB riboswitch aptamer domain, 68 kDa marine metagenome RNA
Buffer: 50 mM MES pH 6.0, 10 mM KCl, 1 mM MgCl2, 4-18 μM coenzyme B12 ligand, pH: 6
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Apr 18
Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14(1):714 (2023)
Ding J, Lee YT, Bhandari Y, Schwieters CD, Fan L, Yu P, Tarosov SG, Stagno JR, Ma B, Nussinov R, Rein A, Zhang J, Wang YX
RgGuinier 5.7 nm
Dmax 19.7 nm
VolumePorod 230 nm3

SASDQ88 – recombinant p123 expressed protein (Gli123)

p123 expressed protein experimental SAS data
DAMMIN model
Sample: P123 expressed protein dimer, 248 kDa Mycoplasma mobile (strain … protein
Buffer: 100 mM ammonium acetate, pH: 6.8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2019 Oct 25
Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding. J Bacteriol :e0034022 (2023)
Matsuike D, Tahara YO, Nonaka T, Wu HN, Hamaguchi T, Kudo H, Hayashi Y, Arai M, Miyata M
RgGuinier 8.2 nm
Dmax 31.6 nm
VolumePorod 436 nm3

SASDQM4 – CRISPR associated Lon protease (CalpL)

SAVED domain-containing protein experimental SAS data
DAMMIF model
Sample: SAVED domain-containing protein monomer, 58 kDa Sulfurihydrogenibium sp. (strain … protein
Buffer: 20 mM Tris, 50 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Dec 14
Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 614(7946):168-174 (2023)
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G
RgGuinier 3.1 nm
Dmax 10.3 nm
VolumePorod 80 nm3

SASDQP4 – CRISPR associated Lon protease (CalpL) in the presence of cyclic oligoadenylate cA4

SAVED domain-containing protein experimental SAS data
DAMMIF model
Sample: SAVED domain-containing protein monomer, 58 kDa Sulfurihydrogenibium sp. (strain … protein
Buffer: 20 mM Tris, 50 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Apr 8
Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 614(7946):168-174 (2023)
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G
RgGuinier 3.2 nm
Dmax 10.3 nm
VolumePorod 82 nm3

SASDQQ4 – CRISPR associated Lon protease (CalpL) asymmetrically dimerizing in the presence of cyclic oligoadenylate cA4

SAVED domain-containing protein experimental SAS data
SASREF MX model
Sample: SAVED domain-containing protein monomer, 58 kDa Sulfurihydrogenibium sp. (strain … protein
Buffer: 20 mM Tris, 50 mM NaCl, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Apr 8
Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 614(7946):168-174 (2023)
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G
RgGuinier 3.8 nm
Dmax 13.0 nm
VolumePorod 116 nm3

SASDQY4 – DNA-binding protein from starved cells: DgrDpsWT + 24 Zn2+ in 50 mM MOPS pH 7.0, 230 mM NaCl, 5 mM EDTA

DNA protection during starvation, DPS (Ferritin superfamily) experimental SAS data
GASBOR model
Sample: DNA protection during starvation, DPS (Ferritin superfamily) dodecamer, 270 kDa Deinococcus grandis protein
Buffer: 50 mM MOPS, 230 mM NaCl, 5 mM EDTA, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 8
Controlled modulation of the dynamics of the Deinococcus grandis Dps N-terminal tails by divalent metals. Protein Sci :e4567 (2023)
Guerra JPL, Blanchet CE, Vieira BJC, Waerenborgh JC, Jones NC, Hoffmann SV, Pereira AS, Tavares P
RgGuinier 4.5 nm
Dmax 19.5 nm
VolumePorod 453 nm3

SASDMT7 – Lanthionine synthetase C-like protein (MadC)

Lanthionine synthetase C-like protein experimental SAS data
GASBOR model
Sample: Lanthionine synthetase C-like protein monomer, 50 kDa Clostridium sp. Maddingley … protein
Buffer: 50 mM HEPES, 500 mM NaCl, pH: 8
Experiment: SAXS data collected at Xenocs Xeuss 2.0 Q-Xoom, Center for Structural Studies, Heinrich-Heine-University on 2019 Nov 28
The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases Frontiers in Microbiology 13 (2023)
Knospe C, Kamel M, Spitz O, Hoeppner A, Galle S, Reiners J, Kedrov A, Smits S, Schmitt L
RgGuinier 2.3 nm
Dmax 7.8 nm
VolumePorod 78 nm3

SASDWA7 – Dihydroneopterin aldolase from H.pylori (HpDHNA:Pterin)

Dihydroneopterin aldolase experimental SAS data
DAMMIN model
Sample: Dihydroneopterin aldolase tetramer, 55 kDa Helicobacter pylori (strain … protein
Buffer: 25 mM Tris-HCl pH 7.5 and 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Apr 5
Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 5:100095 (2023)
Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X
RgGuinier 2.5 nm
Dmax 7.3 nm
VolumePorod 77 nm3

SASDPW2 – mTIP60-Ba (metal-ion induced 60-mer complex of TIP60 (K67E) mutant with barium ions)

TIP60 (K67E) mutant (metal-ion induced 60-mer complex with barium ions)Barium ion experimental SAS data
DAMMIN model
Sample: TIP60 (K67E) mutant (metal-ion induced 60-mer complex with barium ions), 1066 kDa Artificial protein protein
Barium ion 0, 8 kDa
Buffer: 25 mM HEPES, 100 mM NaCl, 5% glycerol, 5 mM BaCl2, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2021 May 23
Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc (2022)
Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K
RgGuinier 9.6 nm
Dmax 21.8 nm