SASBDB entries for UniProt ID:

SASDTX8 – Streptococcus pyogenes glycine cleavage system H-like protein

UniProt ID: P0DN69 (1-110) Glycine cleavage system H-like protein
Glycine cleavage system H-like protein experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Glycine cleavage system H-like protein monomer, 13 kDa Streptococcus pyogenes serotype … protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT, 5% (v/v) glycerol, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2016 Jul 20
Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains Journal of Biological Chemistry :107770 (2024)
Ariza A, Liu Q, Cowieson N, Ahel I, Filippov D, Rack J
RgGuinier 1.5 nm
Dmax 5.0 nm
VolumePorod 22 nm3

SASDTY8 – Streptococcus pyogenes Protein-ADP-ribose hydrolase

UniProt ID: P0DN70 (1-270) Protein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T)
Protein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T) experimental SAS data
ALPHAFOLD model
Sample: Protein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T) monomer, 30 kDa Streptococcus pyogenes serotype … protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT, 5% (v/v) glycerol, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2016 Jul 20
Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains Journal of Biological Chemistry :107770 (2024)
Ariza A, Liu Q, Cowieson N, Ahel I, Filippov D, Rack J
RgGuinier 2.1 nm
Dmax 7.3 nm
VolumePorod 34 nm3

SASDTZ8 – Streptococcus pyogenes Protein-ADP-ribose hydrolase: glycine cleavage system H-like protein complex

UniProt ID: P0DN69 (1-110) Glycine cleavage system H-like protein

UniProt ID: P0DN70 (1-270) Protein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T)
Glycine cleavage system H-like proteinProtein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T) experimental SAS data
ALPHAFOLD model
Sample: Glycine cleavage system H-like protein monomer, 13 kDa Streptococcus pyogenes serotype … protein
Protein-ADP-ribose hydrolase (D13G, Y23S, T61A, I114S, R177H, I246T) monomer, 30 kDa Streptococcus pyogenes serotype … protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 1 mM DTT, 5% (v/v) glycerol, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2016 Jul 20
Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains Journal of Biological Chemistry :107770 (2024)
Ariza A, Liu Q, Cowieson N, Ahel I, Filippov D, Rack J
RgGuinier 2.4 nm
Dmax 8.4 nm
VolumePorod 53 nm3

SASDU52 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, apo form

UniProt ID: None (None-None) Cereblon-midi
Cereblon-midi experimental SAS data
SWISSMODEL model
Sample: Cereblon-midi monomer, 37 kDa protein
Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Nature Communications 15(1) (2024)
Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
RgGuinier 2.7 nm
Dmax 8.6 nm
VolumePorod 61 nm3

SASDU62 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Mezigdomide

UniProt ID: None (None-None) Cereblon-midi

UniProt ID: None (None-None) mezigdomide
Cereblon-midimezigdomide experimental SAS data
PYMOL model
Sample: Cereblon-midi monomer, 37 kDa protein
Mezigdomide monomer, 1 kDa synthetic construct
Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Nature Communications 15(1) (2024)
Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
RgGuinier 2.3 nm
Dmax 7.3 nm
VolumePorod 60 nm3

SASDU72 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Pomalidomide

UniProt ID: None (None-None) Cereblon-midi

UniProt ID: None (None-None) pomalidomide
Cereblon-midipomalidomide experimental SAS data
Cereblon-midi pomalidomide Kratky plot
Sample: Cereblon-midi monomer, 37 kDa protein
Pomalidomide monomer, 0 kDa synthetic construct
Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Nature Communications 15(1) (2024)
Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
RgGuinier 2.3 nm
Dmax 6.9 nm
VolumePorod 63 nm3

SASDU82 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Iberdomide

UniProt ID: None (None-None) Cereblon-midi

UniProt ID: None (None-None) Iberdomide
Cereblon-midiIberdomide experimental SAS data
Cereblon-midi Iberdomide Kratky plot
Sample: Cereblon-midi monomer, 37 kDa protein
Iberdomide monomer, 0 kDa synthetic construct
Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Nature Communications 15(1) (2024)
Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
RgGuinier 2.4 nm
Dmax 7.7 nm
VolumePorod 68 nm3

SASDU92 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Lenalidomide

UniProt ID: None (None-None) Cereblon-midi

UniProt ID: None (None-None) Lenalidomide
Cereblon-midiLenalidomide experimental SAS data
Cereblon-midi Lenalidomide Kratky plot
Sample: Cereblon-midi monomer, 37 kDa protein
Lenalidomide monomer, 0 kDa synthetic construct
Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Nature Communications 15(1) (2024)
Kroupova A, Spiteri V, Rutter Z, Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A
RgGuinier 2.2 nm
Dmax 6.2 nm
VolumePorod 59 nm3

SASDUA2 – The Z-DNA binding domains Zαβ of Z-DNA binding protein 1 (monomer)

UniProt ID: Q9H171 (1-165) Z-DNA-binding protein 1
Z-DNA-binding protein 1 experimental SAS data
DAMMIF model
Sample: Z-DNA-binding protein 1 monomer, 18 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
ZBP1 condensate formation synergizes Z-NAs recognition and signal transduction. Cell Death Dis 15(7):487 (2024)
Xie F, Wu D, Huang J, Liu X, Shen Y, Huang J, Su Z, Li J
RgGuinier 2.1 nm
Dmax 9.0 nm
VolumePorod 19 nm3

SASDUB2 – The Z-DNA binding domains Zαβ of Z-DNA binding protein 1 (dimer)

UniProt ID: Q9H171 (1-165) Z-DNA-binding protein 1
Z-DNA-binding protein 1 experimental SAS data
DAMMIF model
Sample: Z-DNA-binding protein 1 dimer, 37 kDa Homo sapiens protein
Buffer: 20 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2018 Mar 23
ZBP1 condensate formation synergizes Z-NAs recognition and signal transduction. Cell Death Dis 15(7):487 (2024)
Xie F, Wu D, Huang J, Liu X, Shen Y, Huang J, Su Z, Li J
RgGuinier 3.1 nm
Dmax 13.0 nm
VolumePorod 48 nm3