SASBDB entries for UniProt ID:

SASDH75 – Poly(rC)-binding protein 2 (PCBP2) with bound modified RNA stem loop IV poliovirus IRES (SLIVm) - PCBP2/SLIVm complex

UniProt ID: Q15366 (1-365) Poly(rC)-binding protein 2

UniProt ID: None (None-None) modified stem loop IV poliovirus IRES, nucleotides 278-398
Poly(rC)-binding protein 2modified stem loop IV poliovirus IRES, nucleotides 278-398 experimental SAS data
Poly(rC)-binding protein 2 modified stem loop IV poliovirus IRES, nucleotides 278-398 Kratky plot
Sample: Poly(rC)-binding protein 2 monomer, 40 kDa Homo sapiens protein
Modified stem loop IV poliovirus IRES, nucleotides 278-398 monomer, 41 kDa Human poliovirus 1 … RNA
Buffer: 5 mM HEPES-KOH, 25 mM KCl, 2 mM MgCl2, 2 mM DTT, 4 % glycerol, 0.1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Dec 16
Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res (2020)
Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA
RgGuinier 3.7 nm
Dmax 11.5 nm
VolumePorod 162 nm3

SASDH85 – Truncated poly(rC)-binding protein 2 (PCBP2-ΔKH3) with bound modified RNA stem loop IV poliovirus IRES (SLIVm)

UniProt ID: None (None-None) modified stem loop IV poliovirus IRES, nucleotides 278-398

UniProt ID: Q15366 (1-253) Truncated poly(rC)-binding protein 2 (ΔKH3)

UniProt ID: Q15366 (1-253) Truncated poly(rC)-binding protein 2 (ΔKH3)
modified stem loop IV poliovirus IRES, nucleotides 278-398Truncated poly(rC)-binding protein 2 (ΔKH3)Truncated poly(rC)-binding protein 2 (ΔKH3) experimental SAS data
modified stem loop IV poliovirus IRES, nucleotides 278-398 Truncated poly(rC)-binding protein 2 (ΔKH3) Truncated poly(rC)-binding protein 2 (ΔKH3) Kratky plot
Sample: Modified stem loop IV poliovirus IRES, nucleotides 278-398 monomer, 41 kDa Human poliovirus 1 … RNA
Truncated poly(rC)-binding protein 2 (ΔKH3) monomer, 28 kDa Homo sapiens protein
Truncated poly(rC)-binding protein 2 (ΔKH3) monomer, 28 kDa Homo sapiens protein
Buffer: 5 mM HEPES-KOH, 25 mM KCl, 2 mM MgCl2, 2 mM DTT, 4 % glycerol, 0.1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Jul 1
Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res (2020)
Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA
RgGuinier 3.8 nm
Dmax 12.2 nm
VolumePorod 165 nm3

SASDH95 – Truncated Poly(rC)-binding protein 2 (PCBP2-ΔKH3)

UniProt ID: Q15366 (1-253) Truncated poly(rC)-binding protein 2 (ΔKH3)
Truncated poly(rC)-binding protein 2 (ΔKH3) experimental SAS data
Truncated poly(rC)-binding protein 2 (ΔKH3) Kratky plot
Sample: Truncated poly(rC)-binding protein 2 (ΔKH3) monomer, 28 kDa Homo sapiens protein
Buffer: 5 mM HEPES-KOH, 25 mM KCl, 2 mM MgCl2, 2 mM DTT, 4 % glycerol, 0.1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Jan 1
Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res (2020)
Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA
RgGuinier 2.6 nm
Dmax 9.2 nm
VolumePorod 66 nm3

SASDHA5 – Truncated poly(rC)-binding protein 2 (PCBP2-ΔKH1-KH2) with bound modified RNA stem loop IV poliovirus IRES (SLIVm)

UniProt ID: None (None-None) modified stem loop IV poliovirus IRES, nucleotides 278-398

UniProt ID: Q15366 (11-168) Truncated poly(rC)-binding protein 2 (ΔKH1-KH2)
modified stem loop IV poliovirus IRES, nucleotides 278-398Truncated poly(rC)-binding protein 2 (ΔKH1-KH2) experimental SAS data
modified stem loop IV poliovirus IRES, nucleotides 278-398 Truncated poly(rC)-binding protein 2 (ΔKH1-KH2) Kratky plot
Sample: Modified stem loop IV poliovirus IRES, nucleotides 278-398 monomer, 41 kDa Human poliovirus 1 … RNA
Truncated poly(rC)-binding protein 2 (ΔKH1-KH2) monomer, 18 kDa Homo sapiens protein
Buffer: 5 mM HEPES-KOH, 25 mM KCl, 2 mM MgCl2, 2 mM DTT, 4 % glycerol, 0.1 mM EDTA, pH: 7.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2017 Jul 1
Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res (2020)
Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA
RgGuinier 3.5 nm
Dmax 12.2 nm
VolumePorod 126 nm3

SASDHB5 – RelA Homology Domain of p50/RelA heterodimer

UniProt ID: P25799 (39-350) NF-kappa-B p105 subunit 39-350

UniProt ID: Q04207 (19-321) Transcription factor p65 19-321
NF-kappa-B p105 subunit 39-350Transcription factor p65 19-321 experimental SAS data
MULTIFOXS model
Sample: NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Transcription factor p65 19-321 monomer, 35 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 3.8 nm
Dmax 13.0 nm
VolumePorod 110 nm3

SASDHC5 – Nuclear factor kB p50/RelA heterodimer

UniProt ID: Q04207 (19-549) Transcription factor p65 19-549

UniProt ID: P25799 (39-350) NF-kappa-B p105 subunit 39-350
Transcription factor p65 19-549NF-kappa-B p105 subunit 39-350 experimental SAS data
BILBOMD model
Sample: Transcription factor p65 19-549 monomer, 58 kDa Mus musculus protein
NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 4.6 nm
Dmax 15.3 nm
VolumePorod 183 nm3

SASDHD5 – Transactivation domain of RelA

UniProt ID: Q04207 (340-549) Transcription factor p65 340-549
Transcription factor p65 340-549 experimental SAS data
MULTIFOXS model
Sample: Transcription factor p65 340-549 monomer, 23 kDa Mus musculus protein
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 2.7 nm
Dmax 8.2 nm
VolumePorod 59 nm3

SASDHE5 – Rel Homology Domain of p50/RelA bound to IFN kB site DNA

UniProt ID: P25799 (39-350) NF-kappa-B p105 subunit 39-350

UniProt ID: Q04207 (19-321) Transcription factor p65 19-321

UniProt ID: None (None-None) IFN kB DNA
NF-kappa-B p105 subunit 39-350Transcription factor p65 19-321IFN kB DNA experimental SAS data
NF-kappa-B p105 subunit 39-350 Transcription factor p65 19-321 IFN kB DNA Kratky plot
Sample: NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Transcription factor p65 19-321 monomer, 35 kDa Mus musculus protein
IFN kB DNA monomer, 8 kDa DNA
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 4.3 nm
Dmax 13.0 nm
VolumePorod 237 nm3

SASDHF5 – Rel Homology Domain of p50/RelA bound to Urokinase kB site DNA

UniProt ID: P25799 (39-350) NF-kappa-B p105 subunit 39-350

UniProt ID: Q04207 (19-321) Transcription factor p65 19-321

UniProt ID: None (None-None) Urokinase kB
NF-kappa-B p105 subunit 39-350Transcription factor p65 19-321Urokinase kB experimental SAS data
NF-kappa-B p105 subunit 39-350 Transcription factor p65 19-321 Urokinase kB Kratky plot
Sample: NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
Transcription factor p65 19-321 monomer, 35 kDa Mus musculus protein
Urokinase kB monomer, 8 kDa DNA
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Jun 11
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 4.1 nm
Dmax 13.0 nm
VolumePorod 244 nm3

SASDHG5 – Nuclear factor kB p50/RelA bound to IFN kB site DNA

UniProt ID: Q04207 (19-549) Transcription factor p65 19-549

UniProt ID: P25799 (39-350) NF-kappa-B p105 subunit 39-350

UniProt ID: None (None-None) IFN kB DNA
Transcription factor p65 19-549NF-kappa-B p105 subunit 39-350IFN kB DNA experimental SAS data
Transcription factor p65 19-549 NF-kappa-B p105 subunit 39-350 IFN kB DNA Kratky plot
Sample: Transcription factor p65 19-549 monomer, 58 kDa Mus musculus protein
NF-kappa-B p105 subunit 39-350 monomer, 36 kDa Mus musculus protein
IFN kB DNA monomer, 8 kDa DNA
Buffer: 25 mM Tris.Cl, 150 mM NaCl, 1 mM DTT, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Dec 4
An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem :102349 (2022)
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA
RgGuinier 5.1 nm
Dmax 18.9 nm
VolumePorod 314 nm3