Browse by MODEL: Hybrid

SASDPU6 – Duplex-G4-duplex DNA

Duplex-G4-duplex experimental SAS data
AMBER model
Sample: Duplex-G4-duplex monomer, 29 kDa synthetic construct DNA
Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Jun 16
Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM. Nucleic Acids Res (2023)
Monsen RC, Chua EYD, Hopkins JB, Chaires JB, Trent JO
RgGuinier 3.2 nm
Dmax 13.3 nm
VolumePorod 59 nm3

SASDPV3 – Wild type oxalyl-CoA synthetase Pcs60p (2.5 mg/ml) - hexamer-tetramer equilibrium

Oxalate--CoA ligase experimental SAS data
PYMOL model
Sample: Oxalate--CoA ligase, 363 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Hepes, 150 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Dec 18
Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase. Biol Chem (2023)
Bürgi J, Lill P, Giannopoulou EA, Jeffries CM, Chojnowski G, Raunser S, Gatsogiannis C, Wilmanns M
RgGuinier 4.7 nm
Dmax 13.2 nm
VolumePorod 565 nm3

SASDPW3 – Wild type oxalyl-CoA synthetase Pcs60p (0.5 mg/ml) - tetramer-hexamer equilibrium

Oxalate--CoA ligase experimental SAS data
PYMOL model
Sample: Oxalate--CoA ligase, 363 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Hepes, 150 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Dec 18
Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase. Biol Chem (2023)
Bürgi J, Lill P, Giannopoulou EA, Jeffries CM, Chojnowski G, Raunser S, Gatsogiannis C, Wilmanns M
RgGuinier 4.5 nm
Dmax 13.7 nm
VolumePorod 432 nm3

SASDPX3 – Point mutant K352D oxalyl-CoA synthetase Pcs60p (2.5 mg/ml) - dimer

Oxalate--CoA ligase (K352D) experimental SAS data
PYMOL model
Sample: Oxalate--CoA ligase (K352D) dimer, 121 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Hepes, 150 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Dec 18
Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase. Biol Chem (2023)
Bürgi J, Lill P, Giannopoulou EA, Jeffries CM, Chojnowski G, Raunser S, Gatsogiannis C, Wilmanns M
RgGuinier 3.3 nm
Dmax 11.1 nm
VolumePorod 163 nm3

SASDPY3 – Point mutant K352D oxalyl-CoA synthetase Pcs60p (0.5 mg/ml) - dimer

Oxalate--CoA ligase (K352D) experimental SAS data
PYMOL model
Sample: Oxalate--CoA ligase (K352D) dimer, 121 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Hepes, 150 mM NaCl, 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Dec 18
Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase. Biol Chem (2023)
Bürgi J, Lill P, Giannopoulou EA, Jeffries CM, Chojnowski G, Raunser S, Gatsogiannis C, Wilmanns M
RgGuinier 3.3 nm
Dmax 10.2 nm
VolumePorod 194 nm3

SASDQF5 – Zinc finger protein 410 (ZNF410 full length)

Zinc finger protein 410 experimental SAS data
BILBOMD model
Sample: Zinc finger protein 410 monomer, 52 kDa Homo sapiens protein
Buffer: 20 mM Tris, 250 mM NaCl, 0.1% v/v β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Sep 30
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res (2023)
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X
RgGuinier 3.6 nm
Dmax 12.3 nm
VolumePorod 108 nm3

SASDQH5 – Zinc finger protein 410 (ZNF410 full length) bound to DNA

Zinc finger protein 410DNA (Zinc finger protein 410 recognition sequence) experimental SAS data
BILBOMD model
Sample: Zinc finger protein 410 monomer, 52 kDa Homo sapiens protein
DNA (Zinc finger protein 410 recognition sequence) monomer, 11 kDa DNA
Buffer: 20 mM Tris, 250 mM NaCl, 0.1% v/v β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Sep 30
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res (2023)
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X
RgGuinier 4.4 nm
Dmax 14.3 nm
VolumePorod 76 nm3

SASDQJ5 – Zinc finger protein 410 (ZNF410): N-terminal region with 1-5 zinc fingers

Zinc finger protein 410 experimental SAS data
BILBOMD model
Sample: Zinc finger protein 410 monomer, 40 kDa Homo sapiens protein
Buffer: 20 mM Tris, 250 mM NaCl, 0.1% v/v β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Sep 30
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res (2023)
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X
RgGuinier 3.2 nm
Dmax 10.7 nm
VolumePorod 78 nm3

SASDQK5 – Zinc finger protein 410 (ZNF410): N-terminal region with 1-5 zinc fingers bound to DNA

DNA (Zinc finger protein 410 recognition sequence)Zinc finger protein 410 experimental SAS data
BILBOMD model
Sample: DNA (Zinc finger protein 410 recognition sequence) monomer, 11 kDa DNA
Zinc finger protein 410 monomer, 40 kDa Homo sapiens protein
Buffer: 20 mM Tris, 250 mM NaCl, 0.1% v/v β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Apr 25
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res (2023)
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X
RgGuinier 3.1 nm
Dmax 14.1 nm
VolumePorod 63 nm3

SASDQL5 – Zinc finger protein 410 (ZNF410): C-terminal region with 1-5 zinc fingers

Zinc finger protein 410 experimental SAS data
BILBOMD model
Sample: Zinc finger protein 410 monomer, 29 kDa Homo sapiens protein
Buffer: 20 mM Tris, 250 mM NaCl, 0.1% v/v β-mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Sep 30
Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res (2023)
Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X
RgGuinier 3.0 nm
Dmax 9.6 nm
VolumePorod 58 nm3