SASBDB entries for UniProt ID:

SASDPQ5 – His-tagged L-methionine gamma-lyase from Clostridium tetani

UniProt ID: A0A1L7H888 (1-398) L-methionine gamma-lyase
L-methionine gamma-lyase experimental SAS data
CHIMERA model
Sample: L-methionine gamma-lyase tetramer, 181 kDa Clostridium tetani protein
Buffer: PBS-D2O: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 (D2O buffer), pH: 7.4
Experiment: SANS data collected at YuMO SANS TOF spectrometer, IBR-2, Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research on 2019 May 19
Methionine gamma lyase fused with S3 domain VGF forms octamers and adheres to tumor cells via binding EGFR Biochemical and Biophysical Research Communications :149319 (2023)
Bondarev N, Bagaeva D, Bazhenov S, Buben M, Bulushova N, Ryzhykau Y, Okhrimenko I, Zagryadskaya Y, Maslov I, Anisimova N, Sokolova D, Kuklin A, Pokrovsky V, Manukhov I
RgGuinier 4.0 nm
Dmax 14.9 nm
VolumePorod 232 nm3

SASDPK6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) of SARS-CoV-2 in phosphate conditions

UniProt ID: P0DTC9 (44-180) Nucleoprotein
Nucleoprotein experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein
Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 14(1):3331 (2023)
Korn SM, Dhamotharan K, Jeffries CM, Schlundt A
RgGuinier 1.6 nm
Dmax 6.1 nm
VolumePorod 23 nm3

SASDP59 – BTB domain of longitudinals lacking (LOLA) protein

UniProt ID: P42283 (1-120) Longitudinals lacking protein, isoform G
Longitudinals lacking protein, isoform G experimental SAS data
ALPHAFOLD model
Sample: Longitudinals lacking protein, isoform G hexamer, 92 kDa Drosophila melanogaster protein
Buffer: 20 mM Tris, pH 7.4, 200 mM NaCl, 1 mM DTT, pH: 7.4
Experiment: SAXS data collected at BM29, ESRF on 2016 Jul 20
The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers. Elife 13 (2024)
Bonchuk AN, Balagurov KI, Baradaran R, Boyko KM, Sluchanko NN, Khrustaleva AM, Burtseva AD, Arkova OV, Khalisova KK, Popov VO, Naschberger A, Georgiev PG
RgGuinier 4.1 nm
Dmax 14.5 nm
VolumePorod 189 nm3

SASDQG6 – N-terminal truncation mutant of the periplasmic region of conjugal transfer mating pair stabilization protein TraG* from the R100 plasmid

UniProt ID: A0A0C5PJM1 (497-940) Conjugal transfer mating pair stabilization protein TraG
Conjugal transfer mating pair stabilization protein TraG experimental SAS data
DAMMIF model
Sample: Conjugal transfer mating pair stabilization protein TraG monomer, 52 kDa Shigella flexneri 4c protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5% glycerol, pH: 7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 23
Solution characterization of the dynamic conjugative entry exclusion protein TraG Structural Dynamics 9(6):064702 (2022)
Bragagnolo N, Audette G
RgGuinier 4.1 nm
Dmax 17.5 nm
VolumePorod 130 nm3

SASDQ47 – N-terminal GST-like domain of Plasmodium berghei tRNA import protein

UniProt ID: A0A509ARF0 (2-202) tRNA import protein tRIP
tRNA import protein tRIP experimental SAS data
CORAL model
Sample: TRNA import protein tRIP dimer, 49 kDa Plasmodium berghei (strain … protein
Buffer: 25 mM HEPES-NaOH, 300 mM NaCl, 5% (v/v) glycerol, 0.005% (m/v) n-dodecyl beta-D-maltoside, 5 mM 2-mercaptoethanol, pH: 7
Experiment: SAXS data collected at SWING, SOLEIL on 2021 Oct 9
Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes. Protein Sci :e4564 (2023)
Jaramillo Ponce JR, Théobald-Dietrich A, Bénas P, Paulus C, Sauter C, Frugier M
RgGuinier 2.9 nm
Dmax 11.0 nm
VolumePorod 68 nm3

SASDQ59 – Mutant 7-deazapurine in DNA protein A (D95A)

UniProt ID: P0DW33 (2-416) DNA-guanine transglycosylase - D95A mutant
DNA-guanine transglycosylase - D95A mutant experimental SAS data
GROMACS model
Sample: DNA-guanine transglycosylase - D95A mutant monomer, 50 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.7 nm
Dmax 10.1 nm
VolumePorod 67 nm3

SASDRH5 – A ssr1698 Dri1 hemoprotein, wild-type (as-purified) variant

UniProt ID: P73129 (1-96) Ssr1698 protein
Ssr1698 protein experimental SAS data
Sample: Ssr1698 protein monomer, 11 kDa Synechocystis sp. (strain … protein
Buffer: 50 mM Hepes, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2021 Dec 12
A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 15(1):3167 (2024)
Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE
RgGuinier 1.6 nm
Dmax 5.3 nm
VolumePorod 12 nm3

SASDRJ6 – SH2-SH3-SH2 domains of Ras GTPase-activating protein 1 (p120RasGAP)

UniProt ID: P20936 (174-444) Ras GTPase-activating protein 1 (C236S, C261S, C372S, C402S)
Ras GTPase-activating protein 1 (C236S, C261S, C372S, C402S) experimental SAS data
Ras GTPase-activating protein 1 (C236S, C261S, C372S, C402S) Kratky plot
Sample: Ras GTPase-activating protein 1 (C236S, C261S, C372S, C402S) monomer, 31 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8, 350 mM NaCl, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Dec 12
Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP and Dok1 Journal of Biological Chemistry :105098 (2023)
Vish K, Stiegler A, Boggon T
RgGuinier 2.5 nm
Dmax 9.8 nm
VolumePorod 42 nm3

SASDRS7 – Radical SAM enzyme peptide epimerase in the presence of SAM (S-adenosyl-L-methionine)

UniProt ID: Q45595 (1-319) Putative peptide biosynthesis protein YydG
Putative peptide biosynthesis protein YydG experimental SAS data
DADIMODO model
Sample: Putative peptide biosynthesis protein YydG dimer, 80 kDa Bacillus subtilis (strain … protein
Buffer: 25 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2022 Nov 29
Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol (2023)
Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A
RgGuinier 2.9 nm
Dmax 11.8 nm
VolumePorod 115 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

UniProt ID: O28951 (1-427) Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein)

UniProt ID: A0A075WKW4 (1-250) Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains)

UniProt ID: None (None-None) 5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288)
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