SASBDB entries for UniProt ID:

SASDPA3 – K63-linked tetraubiquitin (Ub4)

UniProt ID: P0CG47 (1-76) Polyubiquitin-B
Polyubiquitin-B experimental SAS data
Polyubiquitin-B Kratky plot
Sample: Polyubiquitin-B monomer, 34 kDa Homo sapiens protein
Buffer: 20 mM sodium phosphate, 0.5 mM EDTA, 0.02% NaN3, pH: 6.8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 8
Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep :e55056 (2022)
Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA
RgGuinier 3.2 nm
Dmax 13.0 nm
VolumePorod 44 nm3

SASDPB3 – M1-linked tetraubiquitin (Ub4)

UniProt ID: P0CG47 (1-76) Polyubiquitin-B
Polyubiquitin-B experimental SAS data
Polyubiquitin-B Kratky plot
Sample: Polyubiquitin-B monomer, 34 kDa Homo sapiens protein
Buffer: 20 mM sodium phosphate, 0.5 mM EDTA, 0.02% NaN3, pH: 6.8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 8
Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep :e55056 (2022)
Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA
RgGuinier 3.2 nm
Dmax 12.0 nm
VolumePorod 46 nm3

SASDPC3 – HOTag6 tetramerization domain followed by a 10-Gly linker and monoubiquitin

UniProt ID: P0CG47 (1-76) Polyubiquitin-B
Polyubiquitin-B experimental SAS data
Polyubiquitin-B Kratky plot
Sample: Polyubiquitin-B tetramer, 53 kDa Homo sapiens protein
Buffer: 20 mM sodium phosphate, 0.5 mM EDTA, 0.02% NaN3, pH: 6.8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Oct 8
Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep :e55056 (2022)
Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA
RgGuinier 3.8 nm
Dmax 14.0 nm
VolumePorod 115 nm3

SASDPE3 – GST-Endonuclease 8 2/Single-stranded DNA-binding protein (Nei2-SSB) complex

UniProt ID: P9WNC1 (1-255) Endonuclease 8 2

UniProt ID: P9WGD5 (1-164) Single-stranded DNA-binding protein
Endonuclease 8 2Single-stranded DNA-binding protein experimental SAS data
DAMMIF model
Sample: Endonuclease 8 2 dimer, 108 kDa Mycobacterium tuberculosis (strain … protein
Single-stranded DNA-binding protein octamer, 139 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Jul 10
Identification and characterization of MtbNei2-SSB forms novel pre-replicative BER complex in Mycobacterium tuberculosis.
Jyoti Vishwakarma
RgGuinier 5.5 nm
Dmax 21.0 nm
VolumePorod 734 nm3

SASDPF3 – Receptor-type tyrosine-protein phosphatase kappa extracellular domains (PTPRK-ECDs)

UniProt ID: Q15262 (28-752) Receptor-type tyrosine-protein phosphatase kappa
Receptor-type tyrosine-protein phosphatase kappa experimental SAS data
DAMMIN model
Sample: Receptor-type tyrosine-protein phosphatase kappa monomer, 82 kDa Homo sapiens protein
Buffer: 50 mM MES, 250 mM NaCl, 3% v/v glycerol,, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Dec 13
Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains Journal of Biological Chemistry :102750 (2022)
Hay I, Shamin M, Caroe E, Mohammed A, Svergun D, Jeffries C, Graham S, Sharpe H, Deane J
RgGuinier 7.0 nm
Dmax 26.0 nm
VolumePorod 252 nm3

SASDPG3 – Receptor-type tyrosine-protein phosphatase mu extracellular domains (PTPRM-ECDs)

UniProt ID: P28827 (19-742) Receptor-type tyrosine-protein phosphatase mu
Receptor-type tyrosine-protein phosphatase mu experimental SAS data
DAMMIN model
Sample: Receptor-type tyrosine-protein phosphatase mu monomer, 82 kDa Homo sapiens protein
Buffer: 50 mM MES, 250 mM NaCl, 3% v/v glycerol,, pH: 6
Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Dec 13
Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains Journal of Biological Chemistry :102750 (2022)
Hay I, Shamin M, Caroe E, Mohammed A, Svergun D, Jeffries C, Graham S, Sharpe H, Deane J
RgGuinier 7.2 nm
Dmax 26.0 nm
VolumePorod 255 nm3

SASDPH3 – Benchmarking extraction methods of scattering patterns of poorly resolved components from a SEC-SAXS dataset of BSA.

UniProt ID: P02769 (25-607) Bovine Serum Albumin
Bovine Serum Albumin experimental SAS data
Bovine Serum Albumin Kratky plot
Sample: Bovine Serum Albumin trimer, 199 kDa Bos taurus protein
Buffer: 20 mM Hepes, 150mM NaCl, pH: 7.4
Experiment: SAXS data collected at SWING, SOLEIL on 2021 Sep 24
SEC-SAXS: Experimental set-up and software developments build up a powerful tool. Methods Enzymol 677:221-249 (2022)
Pérez J, Thureau A, Vachette P
RgGuinier 5.2 nm
Dmax 17.6 nm
VolumePorod 370 nm3

SASDPK3 – Vibrio cholerae ParD2:ParE2 complex bound to 21-bp DNA operator box

UniProt ID: P58093 (1-80) Antitoxin ParD

UniProt ID: Q9KMJ0 (1-99) Toxin

UniProt ID: None (None-None) 21-bp DNA operator fragment
Antitoxin ParDToxin21-bp DNA operator fragment experimental SAS data
CUSTOM IN-HOUSE model
Sample: Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein
Toxin, 25 kDa Vibrio cholerae serotype … protein
21-bp DNA operator fragment monomer, 13 kDa Vibrio cholerae O1 DNA
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2020 Jul 18
Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 10(1):eadj2403 (2024)
Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R
RgGuinier 3.2 nm
Dmax 10.0 nm
VolumePorod 140 nm3

SASDPL3 – Vibrio cholerae ParD2:ParE2 complex bound to 31-bp DNA operator box

UniProt ID: P58093 (1-80) Antitoxin ParD

UniProt ID: Q9KMJ0 (1-99) Toxin

UniProt ID: None (None-None) 31-bp DNA operator box
Antitoxin ParDToxin31-bp DNA operator box experimental SAS data
CUSTOM IN-HOUSE model
Sample: Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein
Toxin, 25 kDa Vibrio cholerae serotype … protein
31-bp DNA operator box monomer, 19 kDa Vibrio cholerae O1 DNA
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Dec 4
Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 10(1):eadj2403 (2024)
Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R
RgGuinier 3.3 nm
Dmax 10.5 nm
VolumePorod 160 nm3

SASDPM3 – Vibrio cholerae ParD2:ParE2 complex bound to 33-bp DNA operator fragment

UniProt ID: P58093 (1-80) Antitoxin ParD

UniProt ID: Q9KMJ0 (1-99) Toxin

UniProt ID: None (None-None) 33-bp DNA operator fragment
Antitoxin ParDToxin33-bp DNA operator fragment experimental SAS data
CUSTOM IN-HOUSE model
Sample: Antitoxin ParD hexamer, 54 kDa Vibrio cholerae serotype … protein
Toxin, 25 kDa Vibrio cholerae serotype … protein
33-bp DNA operator fragment monomer, 20 kDa Vibrio cholerae O1 DNA
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2020 Jul 18
Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Sci Adv 10(1):eadj2403 (2024)
Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R
RgGuinier 3.2 nm
Dmax 10.0 nm
VolumePorod 150 nm3