SASBDB entries for UniProt ID:

SASDJX2 – Modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

UniProt ID: None (None-None) cognate hemimethylated 12-bp oligoduplex

UniProt ID: P24200 (1-277) 5-methylcytosine-specific restriction enzyme A
cognate hemimethylated 12-bp oligoduplex5-methylcytosine-specific restriction enzyme A experimental SAS data
SASREF model
Sample: Cognate hemimethylated 12-bp oligoduplex dimer, 15 kDa DNA
5-methylcytosine-specific restriction enzyme A dimer, 65 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 3.9 nm
Dmax 13.5 nm
VolumePorod 69 nm3

SASDJY2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease

UniProt ID: P24200 (1-175) 5-methylcytosine-specific restriction enzyme A (N-terminal domain)
5-methylcytosine-specific restriction enzyme A (N-terminal domain) experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3

SASDJZ2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

UniProt ID: P24200 (1-175) 5-methylcytosine-specific restriction enzyme A (N-terminal domain)

UniProt ID: None (None-None) cognate hemimethylated 12-bp oligoduplex
5-methylcytosine-specific restriction enzyme A (N-terminal domain)cognate hemimethylated 12-bp oligoduplex experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
Cognate hemimethylated 12-bp oligoduplex monomer, 7 kDa DNA
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3

SASDJ33 – Receptor-type tyrosine-protein phosphatase epsilon bound to phospho proto-oncogene tyrosine-protein kinase (rPTPε/phospho-Src complex)

UniProt ID: P23469 (107-400) Receptor-type tyrosine-protein phosphatase epsilon

UniProt ID: P12931 (263-536) Proto-oncogene tyrosine-protein kinase Src, T357M mutant
Receptor-type tyrosine-protein phosphatase epsilonProto-oncogene tyrosine-protein kinase Src, T357M mutant experimental SAS data
CORAL model
Sample: Receptor-type tyrosine-protein phosphatase epsilon monomer, 34 kDa Homo sapiens protein
Proto-oncogene tyrosine-protein kinase Src, T357M mutant monomer, 31 kDa Homo sapiens protein
Buffer: 20 mM Tris , 50 mM NaCl, 5 mM DTT, pH: 8
Experiment: SAXS data collected at 23A1, Taiwan Photon Source, NSRRC on 2017 May 26
An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation Structure (2023)
EswarKumar N, Yang C, Tewary S, Peng W, Chen G, Yeh Y, Yang H, Ho M
RgGuinier 2.9 nm
Dmax 10.0 nm
VolumePorod 60 nm3

SASDJ63 – Streptococcus pneumoniae NADPH oxidase - Tag-free SpNOX

UniProt ID: Q8CZ28-1 (1-400) FAD-binding FR-type domain-containing protein
FAD-binding FR-type domain-containing protein experimental SAS data
OTHER model
Sample: FAD-binding FR-type domain-containing protein monomer, 47 kDa Streptococcus pneumoniae protein
Buffer: 50 mM Tris-HCl pH 7, 300 mM NaCl, 5 mM LMNG, 10 µM FAD, 21.4% D₂O, pH: 7
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2018 Jun 26
Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier. Biophys J 119(3):605-618 (2020)
Vermot A, Petit-Härtlein I, Breyton C, Le Roy A, Thépaut M, Vivès C, Moulin M, Härtlein M, Grudinin S, Smith SME, Ebel C, Martel A, Fieschi F
RgGuinier 3.0 nm
Dmax 10.0 nm
VolumePorod 89 nm3

SASDJ73 – Ubiquitin-like UHRF1 with PHD and RING finger domains (TTD-L2 (123-301))

UniProt ID: Q96T88 (123-301) E3 ubiquitin-protein ligase UHRF1
E3 ubiquitin-protein ligase UHRF1 experimental SAS data
E3 ubiquitin-protein ligase UHRF1 Kratky plot
Sample: E3 ubiquitin-protein ligase UHRF1 monomer, 21 kDa Homo sapiens protein
Buffer: SAXS Buffer, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 Nov 26
Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of its Tandem Tudor Domain Journal of Molecular Biology (2020)
Kori S, Jimenji T, Ekimoto T, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K
RgGuinier 2.0 nm
Dmax 6.6 nm
VolumePorod 26 nm3

SASDJ83 – Phosphorylated ubiquitin-like UHRF1 with PHD and RING finger domains (phTTD-L2 (123-301)

UniProt ID: Q96T88 (123-301) E3 ubiquitin-protein ligase UHRF1
E3 ubiquitin-protein ligase UHRF1 experimental SAS data
E3 ubiquitin-protein ligase UHRF1 Kratky plot
Sample: E3 ubiquitin-protein ligase UHRF1 monomer, 21 kDa Homo sapiens protein
Buffer: SAXS buffer, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 Nov 26
Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of its Tandem Tudor Domain Journal of Molecular Biology (2020)
Kori S, Jimenji T, Ekimoto T, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K
RgGuinier 2.1 nm
Dmax 7.0 nm
VolumePorod 29 nm3

SASDJ93 – Ubiquitin carboxyl-terminal hydrolase, MINDY2, wild-type apo-form

UniProt ID: Q8NBR6 (241-504) Ubiquitin carboxyl-terminal hydrolase MINDY-2
Ubiquitin carboxyl-terminal hydrolase MINDY-2 experimental SAS data
CUSTOM IN-HOUSE model
Sample: Ubiquitin carboxyl-terminal hydrolase MINDY-2 monomer, 31 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 23
Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell (2021)
Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y
RgGuinier 2.1 nm
Dmax 6.5 nm
VolumePorod 45 nm3

SASDJA3 – Ubiquitin carboxyl-terminal hydrolase, MINDY2, wild-type bound to mono-ubiquitin

UniProt ID: Q8NBR6 (241-504) Ubiquitin carboxyl-terminal hydrolase MINDY-2

UniProt ID: P0CG48 (1-76) Polyubiquitin-C
Ubiquitin carboxyl-terminal hydrolase MINDY-2Polyubiquitin-C experimental SAS data
CUSTOM IN-HOUSE model
Sample: Ubiquitin carboxyl-terminal hydrolase MINDY-2 monomer, 31 kDa Homo sapiens protein
Polyubiquitin-C monomer, 9 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 23
Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell (2021)
Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y
RgGuinier 2.3 nm
Dmax 6.8 nm
VolumePorod 58 nm3

SASDJB3 – Ubiquitin carboxyl-terminal hydrolase, MINDY2 (C266A mutant), bound to di-ubiquitin

UniProt ID: Q8NBR6 (241-504) Ubiquitin carboxyl-terminal hydrolase C266A mutant

UniProt ID: P0CG48 (1-76) Polyubiquitin-C
Ubiquitin carboxyl-terminal hydrolase C266A mutantPolyubiquitin-C experimental SAS data
CUSTOM IN-HOUSE model
Sample: Ubiquitin carboxyl-terminal hydrolase C266A mutant monomer, 31 kDa Homo sapiens protein
Polyubiquitin-C dimer, 17 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Nov 23
Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell (2021)
Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y
RgGuinier 2.5 nm
Dmax 8.0 nm
VolumePorod 68 nm3