MACROMOLECULE TYPE: heterocomplex

SASDKW9 – Transcription factors USF1 and NF-Y bound to a CCAAT DNA box(50bp)

Upstream stimulatory factor 1Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 50bp experimental SAS data
DAMMIN model
Sample: Upstream stimulatory factor 1 dimer, 50 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 50bp monomer, 31 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2015 Jun 14
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
Bernardini A, Lorenzo M, Chaves-Sanjuan A, Swuec P, Pigni M, Saad D, Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 4.8 nm
Dmax 17.0 nm
VolumePorod 165 nm3

SASDKX9 – Transcription factors MAX and NF-Y bound to a CCAAT DNA box(48bp)

Protein max (Isoform 2, short, 13-21: missing)Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
DAMMIN model
Sample: Protein max (Isoform 2, short, 13-21: missing) dimer, 39 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2012 Dec 10
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
Bernardini A, Lorenzo M, Chaves-Sanjuan A, Swuec P, Pigni M, Saad D, Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 151 nm3

SASDKR7 – Hunchback mRNA translation repression complex of Brat-NHL, Pum-HD, Nanos-ZnF and hb NRE2 RNA

Brain tumor proteinMaternal protein pumilioProtein nanoshunchback mRNA Nanos Response Element 2 experimental SAS data
Brain tumor protein Maternal protein pumilio Protein nanos hunchback mRNA Nanos Response Element 2 Kratky plot
Sample: Brain tumor protein monomer, 32 kDa Drosophila melanogaster protein
Maternal protein pumilio monomer, 38 kDa Drosophila melanogaster protein
Protein nanos monomer, 11 kDa Drosophila melanogaster protein
Hunchback mRNA Nanos Response Element 2 monomer, 7 kDa Drosophila melanogaster RNA
Buffer: 50 mM Tris, 150 mM NaCl, 1 mM DTT, 3% glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Nov 12
Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 49(15):8866-8885 (2021)
Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J
RgGuinier 3.7 nm
Dmax 12.7 nm
VolumePorod 114 nm3

SASDLE5 – RORg2 bound to a Classic-RORgamma Response Element

Retinoid-related orphan receptor-gammaClassic-RORgamma Response Element experimental SAS data
RORg2 bound to a Classic-RORgamma Response Element Rg histogram
Sample: Retinoid-related orphan receptor-gamma monomer, 56 kDa Homo sapiens protein
Classic-RORgamma Response Element dimer, 19 kDa Homo sapiens DNA
Buffer: 25 mM HEPES, 150 mM TCEP, 2% Glycerol, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Nov 20
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement Journal of Molecular Biology :167258 (2021)
Strutzenberg T, Zhu Y, Novick S, Garcia-Ordonez R, Doebelin C, He Y, Ra Chang M, Kamenecka T, Edwards D, Griffin P
RgGuinier 5.5 nm
Dmax 22.9 nm
VolumePorod 132 nm3

SASDLF5 – RORg2 bound to a Variant-RORgamma Response Element

Retinoid-related orphan receptor-gammaVariant-RORgamma Response Element experimental SAS data
RORg2 bound to a Variant-RORgamma Response Element Rg histogram
Sample: Retinoid-related orphan receptor-gamma monomer, 56 kDa Homo sapiens protein
Variant-RORgamma Response Element dimer, 18 kDa Homo sapiens DNA
Buffer: 25 mM HEPES, 150 mM TCEP, 2% Glycerol, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2020 Nov 20
Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement Journal of Molecular Biology :167258 (2021)
Strutzenberg T, Zhu Y, Novick S, Garcia-Ordonez R, Doebelin C, He Y, Ra Chang M, Kamenecka T, Edwards D, Griffin P
RgGuinier 4.4 nm
Dmax 22.1 nm
VolumePorod 112 nm3

SASDK94 – Streptococcus agalactiae transcription factor BusR 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

SASDKH2 – E2F1/DP1 in complex with a 15-mer DNA oligo

Transcription factor E2F115-mer DNA oligo of the human E2F1 promoterE2F dimerization partner 1 experimental SAS data
CUSTOM IN-HOUSE model
Sample: Transcription factor E2F1 monomer, 20 kDa Homo sapiens protein
15-mer DNA oligo of the human E2F1 promoter monomer, 9 kDa DNA
E2F dimerization partner 1 monomer, 29 kDa Homo sapiens protein
Buffer: 50 mM Tris-Cl pH 8.0, 150 mM NaCl and 2 mM DTT, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2019 Oct 19
High Conformational Flexibility of the E2F1/DP1/DNA Complex. J Mol Biol 433(18):167119 (2021)
Saad D, Paissoni C, Chaves-Sanjuan A, Nardini M, Mantovani R, Gnesutta N, Camilloni C
RgGuinier 3.7 nm
Dmax 11.8 nm
VolumePorod 99 nm3

SASDK54 – Signal recognition particle SRP9/14 heterodimer in complex with full length SRP Alu RNA from Plasmodium falciparum

Signal recognition particle 9Signal recognition particle 14Full-length SRP Alu RNA experimental SAS data
MONSA model
Sample: Signal recognition particle 9 monomer, 12 kDa Plasmodium falciparum protein
Signal recognition particle 14 monomer, 12 kDa Plasmodium falciparum protein
Full-length SRP Alu RNA monomer, 38 kDa Plasmodium falciparum RNA
Buffer: 20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM MgCl2, 10 mM KCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 22
Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 4(1):600 (2021)
Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I
RgGuinier 3.5 nm
Dmax 12.0 nm
VolumePorod 120 nm3

SASDK64 – Signal recognition particle SRP9/14 heterodimer in complex with the 5' domain of SRP Alu RNA from Plasmodium falciparum

Signal recognition particle 9Signal recognition particle 14SRP Alu RNA 5' domain experimental SAS data
MONSA model
Sample: Signal recognition particle 9 monomer, 12 kDa Plasmodium falciparum protein
Signal recognition particle 14 monomer, 12 kDa Plasmodium falciparum protein
SRP Alu RNA 5' domain monomer, 24 kDa Plasmodium falciparum RNA
Buffer: 20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM MgCl2, 10 mM KCl, 1mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2018 Jun 22
Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 4(1):600 (2021)
Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I
RgGuinier 3.2 nm
Dmax 11.9 nm
VolumePorod 77 nm3

SASDJ96 – Trinucleosomes from Xenopus laevis (African clawed frog)

Histone H3Histone H4Histone H2A type 1Histone H2BNon-linker Ended Trinucleosome DNA experimental SAS data
Histone H3 Histone H4 Histone H2A type 1 Histone H2B Non-linker Ended Trinucleosome DNA Kratky plot
Sample: Histone H3 monomer, 15 kDa Xenopus laevis protein
Histone H4 monomer, 11 kDa Xenopus laevis protein
Histone H2A type 1 monomer, 14 kDa Xenopus laevis protein
Histone H2B monomer, 14 kDa Xenopus laevis protein
Non-linker Ended Trinucleosome DNA monomer, 172 kDa DNA
Buffer: 20 mM Tris 150 mM NaCl 1 mM EDTA 1 mM DTT 50% w/v sucrose, pH: 7.5
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2016 Mar 11
Solution structure(s) of trinucleosomes from contrast variation SAXS Nucleic Acids Research (2021)
Mauney A, Muthurajan U, Luger K, Pollack L
RgGuinier 12.9 nm
Dmax 41.8 nm