MACROMOLECULE TYPE: heterocomplex

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
AT-rich 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

SASDQE9 – YdaT_toxin domain-containing protein bound to 30 base pair 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
Om 30 base pair 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

SASDQU6 – eukaryotic initiation factor 4A1 bound to 20 nt (AG)10 ssRNA

Eukaryotic initiation factor 4A-I(AG)10-RNA experimental SAS data
Eukaryotic initiation factor 4A-I (AG)10-RNA Kratky plot
Sample: Eukaryotic initiation factor 4A-I monomer, 46 kDa Homo sapiens protein
(AG)10-RNA monomer, 7 kDa synthetic construct RNA
Buffer: 20 mM Hepes, 100 mM KCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Sep 16
eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res (2023)
Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin LM, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M
RgGuinier 2.8 nm
Dmax 10.5 nm
VolumePorod 96 nm3

SASDQV6 – eukaryotic initiation factor 4A1 bound to 20 nt (CAA)6CA ssRNA

Eukaryotic initiation factor 4A-I(CAA)6CA-RNA experimental SAS data
Eukaryotic initiation factor 4A-I (CAA)6CA-RNA Kratky plot
Sample: Eukaryotic initiation factor 4A-I monomer, 46 kDa Homo sapiens protein
(CAA)6CA-RNA monomer, 6 kDa synthetic construct RNA
Buffer: 20 mM Hepes, 100 mM KCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Jul 22
eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res (2023)
Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin LM, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M
RgGuinier 3.1 nm
Dmax 12.8 nm
VolumePorod 89 nm3

SASDQW6 – multimeric eukaryotic initiation factor 4A1 bound to 20 nt (AG)10 ssRNA

(AG)10-RNAEukaryotic initiation factor 4A-I experimental SAS data
(AG)10-RNA Eukaryotic initiation factor 4A-I Kratky plot
Sample: (AG)10-RNA monomer, 7 kDa synthetic construct RNA
Eukaryotic initiation factor 4A-I trimer, 138 kDa Homo sapiens protein
Buffer: 20 mM Hepes, 100 mM KCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Sep 16
eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res (2023)
Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin LM, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M
RgGuinier 3.4 nm
Dmax 13.1 nm
VolumePorod 150 nm3

SASDQX6 – multimeric eukaryotic initiation factor 4A1 bound to 20 nt (AG)10-24bp duplex RNA

Eukaryotic initiation factor 4A-I(AG)10-24bp loading-RNA(AG)10-24bp duplex-RNA experimental SAS data
Eukaryotic initiation factor 4A-I (AG)10-24bp loading-RNA (AG)10-24bp duplex-RNA Kratky plot
Sample: Eukaryotic initiation factor 4A-I trimer, 138 kDa Homo sapiens protein
(AG)10-24bp loading-RNA monomer, 15 kDa synthetic construct RNA
(AG)10-24bp duplex-RNA monomer, 7 kDa synthetic construct RNA
Buffer: 20 mM Hepes, 100 mM KCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Sep 16
eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res (2023)
Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin LM, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M
RgGuinier 4.9 nm
Dmax 16.2 nm
VolumePorod 230 nm3

SASDNN8 – Upstream of N-ras, isoform A, CSD 7, 8 and 9 from Drosophila melanogaster in complex with a poly(A)-15mer RNA

Upstream of N-ras, isoform ApolyA-15mer experimental SAS data
Upstream of N-ras, isoform A polyA-15mer Kratky plot
Sample: Upstream of N-ras, isoform A monomer, 26 kDa Drosophila melanogaster protein
PolyA-15mer monomer, 5 kDa RNA
Buffer: 20 mM HEPES, 150 mM NaCl, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 8
Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res (2023)
Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J
RgGuinier 2.2 nm
Dmax 7.5 nm
VolumePorod 37 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

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

SASDQM5 – Zinc finger protein 410 (ZNF410): C-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, 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 3.1 nm
Dmax 11.9 nm
VolumePorod 52 nm3