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11 hits found for Tokuda

SASDCT6 – 12N12 nucleosome in 60% sucrose with ADP-BeF3

169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
12N12 nucleosome in 60% sucrose with ADP-BeF3 Rg histogram
Sample: 169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 4.8 nm
Dmax 14.0 nm

SASDCU6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose without any nucleotides added (Apo)

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose without any nucleotides added (Apo) Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.2 nm
Dmax 12.8 nm

SASDCV6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with ADP-BeF3

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with ADP-BeF3 Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, ADP-BeF3 (0.5 mM ADP, 4 mM NaF, 0.6 mM BeCl2), pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.3 nm
Dmax 16.5 nm

SASDCW6 – Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP

Chromodomain-helicase-DNA-binding protein 1169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)Histone H2A type 1Histone H2B 1.1Histone H3.2Histone H4 experimental SAS data
Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP Rg histogram
Sample: Chromodomain-helicase-DNA-binding protein 1 dimer, 266 kDa Saccharomyces cerevisiae protein
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) monomer, 52 kDa DNA
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B 1.1 monomer, 14 kDa Xenopus laevis protein
Histone H3.2 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Buffer: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP, pH: 7.8
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 24
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 46(10):4978-4990 (2018)
Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
RgGuinier 5.6 nm
Dmax 16.7 nm

SASDBS7 – Nucleosome Core Particle: 1.2 M NaCl, 50% sucrose, 50ms - 10s time resolved data

Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B HeterodimerNucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 HeterodimerNucleasome Core Particle with Widom 601 DNA - dsDNA experimental SAS data
Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer Nucleasome Core Particle with Widom 601 DNA - dsDNA Kratky plot
Sample: Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer dimer, 48 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer dimer, 46 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - dsDNA monomer, 92 kDa Xenopus laevis DNA
Buffer: 20 mM Tris-Cl, 0.1 mM EDTA, 0.1 mM DTT, 50% sucrose, 1.2 M NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Apr 14
Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 114(2):334-339 (2017)
...Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 5.8 nm

SASDBT7 – Nucleosome Core Particle: 1.9 M NaCl, 50% sucrose, 50ms - 10s time resolved data

Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B HeterodimerNucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 HeterodimerNucleasome Core Particle with Widom 601 DNA - dsDNA experimental SAS data
Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer Nucleasome Core Particle with Widom 601 DNA - dsDNA Kratky plot
Sample: Nucleasome Core Particle with Widom 601 DNA - HISTONE H2A-H2B Heterodimer dimer, 48 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - HISTONE H3-H4 Heterodimer dimer, 46 kDa Xenopus laevis protein
Nucleasome Core Particle with Widom 601 DNA - dsDNA monomer, 92 kDa Xenopus laevis DNA
Buffer: 20 mM Tris-Cl, 0.1 mM EDTA, 0.1 mM DTT, 50% sucrose, 1.9 M NaCl, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2014 Apr 14
Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 114(2):334-339 (2017)
...Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 6.8 nm

SASDCT9 – Bacteriophage phi-X174 - Empty Capsid

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
...Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 14.0 nm

SASDCU9 – Bacteriophage phi-X174 - Before Reaction with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
...Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.1 nm

SASDCV9 – Bacteriophage phi-X174 - ~45s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
...Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.7 nm

SASDCW9 – Bacteriophage phi-X174 - ~245s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
...Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.9 nm

SASDCX9 – Bacteriophage phi-X174 - ~545s after mixing with LPS

Bacteriophage phi-X174 experimental SAS data
Bacteriophage phi-X174 Kratky plot
Sample: Bacteriophage phi-X174 monomer, 0 kDa protein
Buffer: 0.15 mg/mL LPS, 0.06 M NH4Cl2, 0.09 M NaCl, 0.1 M KCl, 1 mM MgS04, 1 mM CaCl2, 0.1 M Tris-HCl, pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Oct 25
Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 114(52):13708-13713 (2017)
...Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG
RgGuinier 12.9 nm