Browse by MODEL: Hybrid

SASDKV6 – SARS-CoV-2 non-structural protein 10/non-structural protein 16 complex (nsp10/nsp16)

Replicase polyprotein 1a (non-structural protein 10)Replicase polyprotein 1ab (non-structural protein 16) experimental SAS data
GASBOR model
Sample: Replicase polyprotein 1a (non-structural protein 10) monomer, 15 kDa Severe acute respiratory … protein
Replicase polyprotein 1ab (non-structural protein 16) monomer, 33 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 150 mM NaCl, 5 mM MgCl2, 2 mM β-mercaptoethanol, pH: 8.5
Experiment: SAXS data collected at BM29, ESRF on 2020 Dec 11
Despite the odds: formation of the SARS-CoV-2 methylation complex Nucleic Acids Research (2024)
Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones A, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz G, Pyrć K, Czarna A
RgGuinier 2.0 nm
Dmax 8.0 nm
VolumePorod 28 nm3

SASDTP5 – Invariant surface glycoprotein 75 (N134A) amino acids 29-468

Invariant surface glycoprotein (N134A) experimental SAS data
CORAL model
Sample: Invariant surface glycoprotein (N134A) monomer, 49 kDa Trypanosoma brucei protein
Buffer: 20 mM Tris-HCl, 75 mM KCl, pH: 7.6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Aug 18
Trypanosoma brucei Invariant Surface Glycoprotein 75 Is an Immunoglobulin Fc Receptor Inhibiting Complement Activation and Antibody-Mediated Cellular Phagocytosis. J Immunol (2024)
Mikkelsen JH, Stødkilde K, Jensen MP, Hansen AG, Wu Q, Lorentzen J, Graversen JH, Andersen GR, Fenton RA, Etzerodt A, Thiel S, Andersen CBF
RgGuinier 3.6 nm
Dmax 15.0 nm
VolumePorod 127 nm3

SASDF33 – Antigen 43/Fragment antigen-binding region Fab10C12 complex (Ag43-Fab)

Alpha domain of Ag43aFragment antigen-binding region Fab10C12 experimental SAS data
DAMFILT model
Sample: Alpha domain of Ag43a monomer, 49 kDa Escherichia coli protein
Fragment antigen-binding region Fab10C12 monomer, 47 kDa Mus musculus protein
Buffer: 25 mM HEPES, 150 mM NaCl, pH: 7
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Nov 3
Inhibition of aggregation and biofilm formation by Uropathogenic Escherichia coli
Andrew Whitten
RgGuinier 4.3 nm
Dmax 15.0 nm
VolumePorod 103 nm3

SASDRG9 – Stromal cell-derived factor 1, CXCL12

Stromal cell-derived factor 1 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Stromal cell-derived factor 1 monomer, 9 kDa Homo sapiens protein
Buffer: 20 mM Tris, 50 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2021 Nov 11
The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12. Nat Commun 15(1):1201 (2024)
Mantonico MV, De Leo F, Quilici G, Colley LS, De Marchis F, Crippa M, Mezzapelle R, Schulte T, Zucchelli C, Pastorello C, Carmeno C, Caprioglio F, Ricagno S, Giachin G, Ghitti M, Bianchi ME, Musco G
RgGuinier 1.5 nm
Dmax 4.8 nm
VolumePorod 19 nm3

SASDTC5 – Full-length E3 ubiquitin-protein ligase HACE1

E3 ubiquitin-protein ligase HACE1 experimental SAS data
GASBOR model
Sample: E3 ubiquitin-protein ligase HACE1 dimer, 205 kDa Homo sapiens protein
Buffer: 50 mM HEPES, 50 mM NaCl, 5 mM DTT, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2023 Apr 21
Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1 Nature Structural & Molecular Biology (2024)
Düring J, Wolter M, Toplak J, Torres C, Dybkov O, Fokkens T, Bohnsack K, Urlaub H, Steinchen W, Dienemann C, Lorenz S
RgGuinier 5.2 nm
Dmax 16.4 nm
VolumePorod 379 nm3

SASDTD5 – N-terminally truncated E3 ubiquitin-protein ligase HACE1

E3 ubiquitin-protein ligase HACE1 experimental SAS data
MULTIFOXS model
Sample: E3 ubiquitin-protein ligase HACE1 monomer, 100 kDa Homo sapiens protein
Buffer: 50 mM HEPES, 50 mM NaCl, 5 mM DTT, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2023 Apr 21
Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1 Nature Structural & Molecular Biology (2024)
Düring J, Wolter M, Toplak J, Torres C, Dybkov O, Fokkens T, Bohnsack K, Urlaub H, Steinchen W, Dienemann C, Lorenz S
RgGuinier 4.6 nm
Dmax 17.8 nm
VolumePorod 219 nm3

SASDUK2 – Histone deacetylase 7

Histone deacetylase 7 experimental SAS data
COOT model
Sample: Histone deacetylase 7 monomer, 44 kDa Arabidopsis thaliana protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 24
Structure-function analyses reveal Arabidopsis thaliana HDA7 to be an inactive histone deacetylase Current Research in Structural Biology :100136 (2024)
Saharan K, Baral S, Shaikh N, Vasudevan D
RgGuinier 3.0 nm
Dmax 10.2 nm
VolumePorod 85 nm3

SASDT82 – Halophilic Lrp transcription factor

AsnC family transcriptional regulator experimental SAS data
PHENIX model
Sample: AsnC family transcriptional regulator dimer, 36 kDa Haloferax mediterranei (strain … protein
Buffer: 50 mM Tris, 1.5 M NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2021 Nov 12
Global Lrp regulator protein from Haloferax mediterranei: Transcriptional analysis and structural characterization. Int J Biol Macromol :129541 (2024)
Matarredona L, García-Bonete MJ, Guío J, Camacho M, Fillat MF, Esclapez J, Bonete MJ
RgGuinier 2.4 nm
Dmax 7.9 nm
VolumePorod 70 nm3

SASDRX8 – Heterodimeric complex of AfAgo protein Af1318 and AfAgo-N protein (containing N-L1-L2 domains) with a 14 base pair DNA oligoduplex in low salt buffer

Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein)Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains)5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein) monomer, 51 kDa Archaeoglobus fulgidus (strain … protein
Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains) monomer, 31 kDa Archaeoglobus fulgidus DSM … protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH 7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 2.9 nm
Dmax 9.7 nm
VolumePorod 145 nm3

SASDRY8 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant complexed with a 14 base pair DNA oligoduplex in low salt buffer

single-chain full Archaeoglobus fulgidus Argonaute5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
GASBOR model
Sample: Single-chain full Archaeoglobus fulgidus Argonaute monomer, 78 kDa Archaeoglobus fulgidus protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 3.0 nm
Dmax 10.3 nm
VolumePorod 131 nm3