Search

  
Advanced search  

24 hits found for dsDNA

SASDBF2 – ...dsDNA-Sa Oligonucleotide

40bp long dsDNA-Sa Oligonucleotide experimental SAS data
DAMMIN model
Sample: ...dsDNA-Sa Oligonucleotide monomer, 25 kDa DNA
Buffer: 0.5 x Tris/Borate/EDTA (TBE), pH:
Experiment: SAXS data collected at BM29, ESRF on 2015 Aug 28
Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius. Mol Microbiol 105(5):777-793 (2017)
Li L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV
RgGuinier 3.6 nm
Dmax 12.0 nm

SASDBJ2 – ...dsDNA-Sa oligonucleotide.

40bp long dsDNA-Sa OligonucleotideWild-type archaeal biofilm regulator 1 (ABfR1: Transcriptional regulator ArsR family). experimental SAS data
DAMMIN model
Sample: ...dsDNA-Sa Oligonucleotide monomer, 25 kDa DNA
Wild-type archaeal biofilm regulator 1 (ABfR1: Transcriptional regulator ArsR family). dimer, 26 kDa Sulfolobus acidocaldarius protein
Buffer: 0.5 x Tris/Borate/EDTA (TBE), pH:
Experiment: SAXS data collected at BM29, ESRF on 2015 Aug 27
Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius. Mol Microbiol 105(5):777-793 (2017)
Li L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV
RgGuinier 3.0 nm
Dmax 11.8 nm

SASDDG3 – Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA

Sa0446 binding sequence 40bpTranscriptional regulator Lrs14-like protein experimental SAS data
DAMMIF model
Sample: Sa0446 binding sequence 40bp monomer, 25 kDa DNA
Transcriptional regulator Lrs14-like protein dimer, 33 kDa Sulfolobus acidocaldarius protein
Buffer: 300 mM NaCl, 20 mM HEPES, pH 7.5, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 5
Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with 40 bp DNA
Marian Vogt
RgGuinier 3.4 nm
Dmax 12.8 nm
VolumePorod 60 nm3

SASDML3 – Mycobacterium phage TipsytheTRex immunity repressor bound to 24mer DNA

Immunity repressor24mer dsDNA experimental SAS data
BILBOMD model
Sample: Immunity repressor monomer, 21 kDa Mycobacterium phage TipsytheTRex protein
...dsDNA monomer, 15 kDa DNA
Buffer: 20 mM Tris pH 7.5, 0.5 M NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Sep 10
A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence. Nat Commun 13(1):4105 (2022)
McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR
RgGuinier 2.4 nm
Dmax 9.0 nm
VolumePorod 43 nm3

SASDMM3 – Mycobacterium phage TipsytheTRex immunity repressor mixed with 13mer DNA

Immunity repressor13mer dsDNA experimental SAS data
BILBOMD model
Sample: Immunity repressor monomer, 21 kDa Mycobacterium phage TipsytheTRex protein
...dsDNA monomer, 8 kDa DNA
Buffer: 20 mM Tris pH 7.5, 0.5 M NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Dec 10
A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence. Nat Commun 13(1):4105 (2022)
McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR
RgGuinier 2.0 nm
Dmax 8.5 nm
VolumePorod 18 nm3

SASDBX3 – ...dsDNA

Aureobox dsDNA experimental SAS data
DAMFILT model
Sample: ...dsDNA monomer, 13 kDa synthetic construct DNA
Buffer: 50 mM Tris 50 mM boric acid 1 mM EDTA, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 2.0 nm
Dmax 8.6 nm
VolumePorod 18 nm3

SASDBZ3 – Aureochrome 1a bZIP-LOV module: PtAUREO1a bZIP-LOV (Light oxygen voltage)/DNA complex (light state)

Aureobox dsDNAAureochrome 1a bZIP-LOV module experimental SAS data
DAMFILT model
Sample: ...dsDNA monomer, 13 kDa synthetic construct DNA
Aureochrome 1a bZIP-LOV module dimer, 57 kDa Phaeodactylum tricornutum protein
Buffer: 50 mM Tris 50 mM boric acid 1 mM EDTA, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2014 Nov 6
Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes. Nucleic Acids Res 44(12):5957-70 (2016)
Banerjee A, Herman E, Serif M, Maestre-Reyna M, Hepp S, Pokorny R, Kroth PG, Essen LO, Kottke T
RgGuinier 4.5 nm
Dmax 16.7 nm
VolumePorod 97 nm3

SASDV54 – ...dsDNA.

Phage antirepressor protein CroIR1 22 base pair dsDNA experimental SAS data
OTHER [STATIC IMAGE] model
Sample: Phage antirepressor protein Cro dimer, 24 kDa Escherichia coli O157:H7 protein
...dsDNA monomer, 14 kDa DNA
Buffer: 20 mM sodium acetate, 150 mM NaCl, 1 mM TCEP, pH: 5.5
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 13
Structural-function relationship of YdaS, a Cro-type repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7
Marusa Prolic Kalinsek
RgGuinier 2.8 nm
Dmax 10.1 nm
VolumePorod 53 nm3

SASDP74 – AT-rich DNA

AT-rich dsDNA experimental SAS data
DAMMIN model
Sample: ...dsDNA monomer, 7 kDa DNA
Buffer: 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 6
Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome. Life Sci Alliance 6(3) (2023)
Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG
RgGuinier 1.7 nm
Dmax 4.6 nm
VolumePorod 12 nm3

SASDP84 – SALL4 Zinc Finger Cluster 4 bound to AT-rich DNA

Sal-like protein 4AT-rich dsDNA experimental SAS data
OTHER model
Sample: Sal-like protein 4 monomer, 8 kDa Mus musculus protein
...dsDNA monomer, 7 kDa DNA
Buffer: 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2020 Feb 6
Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome. Life Sci Alliance 6(3) (2023)
Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG
RgGuinier 1.8 nm
Dmax 5.1 nm
VolumePorod 14 nm3

SASDK94 – ...dsDNA complex

Transcriptional repressor BusRBusR Recognition sequence experimental SAS data
OTHER model
Sample: Transcriptional repressor BusR tetramer, 95 kDa Streptococcus agalactiae protein
BusR Recognition sequence monomer, 28 kDa synthetic construct DNA
Buffer: 20mM HEPES, pH6.5, 100mM NaCl, 3% glycerol (v/v), pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 2
BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Res (2021)
Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G
RgGuinier 4.3 nm
Dmax 14.2 nm
VolumePorod 210 nm3

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
...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)
Chen Y, Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 5.8 nm

SASDLS7 – Mycobacterium phage TipsytheTRex immunity repressor bound to DNA

Immunity repressor21mer dsDNA experimental SAS data
BILBOMD model
Sample: Immunity repressor monomer, 21 kDa Mycobacterium phage TipsytheTRex protein
...dsDNA monomer, 13 kDa DNA
Buffer: 20 mM Tris pH 7.5, 0.5 M NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Sep 10
A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence. Nat Commun 13(1):4105 (2022)
McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR
RgGuinier 2.3 nm
Dmax 7.4 nm
VolumePorod 41 nm3

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
...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)
Chen Y, Tokuda JM, Topping T, Meisburger SP, Pabit SA, Gloss LM, Pollack L
RgGuinier 6.8 nm

SASDH39 – ...dsDNA (5'p-ATTGTACGTACAAT)

Piwi protein AF_13185'-phosphorilated 14-mer DNA oligoduplex experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Piwi protein AF_1318 dimer, 102 kDa Archaeoglobus fulgidus protein
5'-phosphorilated 14-mer DNA oligoduplex dimer, 9 kDa DNA
Buffer: 20 mM TrisHCl, pH 7.5, 5 mM MgCl2, 150 mM NaCl and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 11(1):4518 (2021)
Golovinas E, Rutkauskas D, Manakova E, Jankunec M, Silanskas A, Sasnauskas G, Zaremba M
RgGuinier 3.2 nm
Dmax 10.1 nm
VolumePorod 158 nm3

SASDH49 – ...dsDNA (5'p-ATTGTACGTACAAT)

Piwi protein AF_1318 delta (296-303) mutant5'-phosphorilated 14-mer DNA oligoduplex experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Piwi protein AF_1318 delta (296-303) mutant monomer, 50 kDa Archaeoglobus fulgidus protein
5'-phosphorilated 14-mer DNA oligoduplex dimer, 9 kDa DNA
Buffer: 20 mM TrisHCl, pH 7.5, 5 mM MgCl2, 150 mM NaCl and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 11(1):4518 (2021)
Golovinas E, Rutkauskas D, Manakova E, Jankunec M, Silanskas A, Sasnauskas G, Zaremba M
RgGuinier 2.8 nm
Dmax 9.6 nm
VolumePorod 109 nm3

SASDQE9 – ...dsDNA

YdaT_toxin domain-containing proteinOm 30 base pair dsDNA experimental SAS data
OTHER model
Sample: YdaT_toxin domain-containing protein tetramer, 74 kDa Escherichia coli O157:H7 protein
...dsDNA dimer, 37 kDa DNA
Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 14
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7 Acta Crystallographica Section D Structural Biology 79(3):245-258 (2023)
Prolič-Kalinšek M, Volkov A, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R
RgGuinier 4.2 nm
Dmax 12.8 nm
VolumePorod 190 nm3

SASDMH9 – ...dsDNA binding sequence (SANS data at 0% D2O)

Multidrug resistance operon repressor34 base pair double-stranded DNA experimental SAS data
MONSA model
Sample: Multidrug resistance operon repressor dimer, 32 kDa Pseudomonas aeruginosa protein
34 base pair double-stranded DNA monomer, 21 kDa synthetic construct DNA
Buffer: 20mM NaPO4, 150 mM NaCl, 10 mM DTT, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2018 May 30
Small-angle X-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model Biophysical Journal (2022)
Caporaletti F, Pietras Z, Morad V, Mårtensson L, Gabel F, Wallner B, Martel A, Sunnerhagen M
RgGuinier 2.9 nm
Dmax 7.8 nm
VolumePorod 79 nm3

SASDBB7 – Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

Endonuclease 8-like 1dsDNA experimental SAS data
DAMMIN model
Sample: Endonuclease 8-like 1 monomer, 45 kDa Homo sapiens protein
dsDNA monomer, 2 kDa DNA
Buffer: 25mM HEPES 100mM NaCl 1mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jan 20
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.3 nm
Dmax 17.5 nm
VolumePorod 92 nm3

SASDQ79 – Mutant 7-deazapurine in DNA protein A (D95A) bound to a 28 base pair DNA substrate (2-state model: complex plus free DNA)

Custom 28 base pair double stranded DNADNA-guanine transglycosylase - D95A mutant experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
DNA-guanine transglycosylase - D95A mutant monomer, 50 kDa Salmonella enterica subsp. … protein
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 3.4 nm
Dmax 13.5 nm
VolumePorod 104 nm3

SASDBA7 – Human NEI like DNA glycosylase 1 (NEIL1) bound to Proliferating Cell Nuclear Antigen (PCNA) and DNA

Endonuclease 8-like 1dsDNAProliferating cell nuclear antigen experimental SAS data
DAMMIN model
Sample: Endonuclease 8-like 1 monomer, 45 kDa Homo sapiens protein
dsDNA monomer, 2 kDa DNA
Proliferating cell nuclear antigen monomer, 30 kDa Homo sapiens protein
Buffer: 25mM HEPES 100mM NaCl 1mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Jan 20
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 45(5):2897-2909 (2017)
Prakash A, Moharana K, Wallace SS, Doublié S
RgGuinier 3.4 nm
Dmax 16.4 nm
VolumePorod 113 nm3

SASDQ69 – 28 base pair DNA substrate (used in experiments with 7-deazapurine in DNA proteins)

Custom 28 base pair double stranded DNA experimental SAS data
GROMACS model
Sample: Custom 28 base pair double stranded DNA monomer, 17 kDa Synthetic, purchased from … DNA
Buffer: 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH: 7
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2021 Dec 22
7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res (2023)
Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D
RgGuinier 2.6 nm
Dmax 10.2 nm
VolumePorod 24 nm3

SASDJZ4 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer )

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
dsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 6.5 nm
Dmax 23.1 nm
VolumePorod 1090 nm3

SASDJ25 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer/dimer)

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5DNA-dependent protein kinase catalytic subunitdsDNA experimental SAS data
BILBOMD model
Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein
X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein
DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein
dsDNA dimer, 21 kDa DNA
Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol (2020)
Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA
RgGuinier 7.5 nm
Dmax 29.4 nm
VolumePorod 1440 nm3