MACROMOLECULE TYPE: heterocomplex

SASDJT4 – Complex of Candidatus Glomeribacter gigasporarum cyclodipeptide synthase (Cglo-CDPS) with Phe-tRNAPhe

Candidatus Glomeribacter gigasporarum cyclodipeptide synthaseE. coli Phe-tRNAPhe experimental SAS data
Candidatus Glomeribacter gigasporarum cyclodipeptide synthase E. coli Phe-tRNAPhe Kratky plot
Sample: Candidatus Glomeribacter gigasporarum cyclodipeptide synthase monomer, 34 kDa Candidatus Glomeribacter gigasporarum protein
E. coli Phe-tRNAPhe monomer, 25 kDa Escherichia coli RNA
Buffer: 10 mM MOPS pH6.7; 200 mM NaCl, 8 mM MgCl2, pH: 6.7
Experiment: SAXS data collected at SWING, SOLEIL on 2016 Oct 2
Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. RNA 26(11):1589-1602 (2020)
Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E
RgGuinier 3.3 nm
Dmax 14.0 nm
VolumePorod 77 nm3

SASDJW7 – pri-miR16-1 primary microRNA in complex with DGCR8-core protein

primary microRNA pri-miR16-1 complexed with DGCR8-core proteinMicroprocessor complex subunit DGCR8 experimental SAS data
DAMMIF model
Sample: Primary microRNA pri-miR16-1 complexed with DGCR8-core protein monomer, 36 kDa Homo sapiens RNA
Microprocessor complex subunit DGCR8 monomer, 26 kDa Homo sapiens protein
Buffer: 50 mM KCl, 50 mM HEPES, 5 mM DTT, 1% glycerol, 50% sucrose, DGCR8-core, pH: 7.5
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2017 Apr 12
Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures Biophysical Journal (2020)
Pabit S, Chen Y, Usher E, Cook E, Pollack L, Showalter S
RgGuinier 5.0 nm
Dmax 17.2 nm
VolumePorod 125 nm3

SASDJW4 – X-ray repair cross-complementing proteins 5 and 6-DNA

X-ray repair cross-complementing protein 6X-ray repair cross-complementing protein 5Y-DNA 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
Y-DNA monomer, 18 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 2010 Jan 8
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 4.1 nm
Dmax 14.8 nm
VolumePorod 280 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

SASDFT8 – The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element HoxB13 DR0

Retinoic acid receptor alpha, RARRetinoic acid receptor RXR-alphaDNA response element HoxB13 DR0 experimental SAS data
CORAL model
Sample: Retinoic acid receptor alpha, RAR monomer, 41 kDa Mus musculus protein
Retinoic acid receptor RXR-alpha monomer, 38 kDa Mus musculus protein
DNA response element HoxB13 DR0 monomer, 10 kDa DNA
Buffer: 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 19
Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR Nucleic Acids Research (2020)
Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N
RgGuinier 3.8 nm
Dmax 14.5 nm
VolumePorod 132 nm3

SASDFU8 – The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element F11r DR5.

Retinoic acid receptor alpha, RARRetinoic acid receptor RXR-alphaDNA response element F11r DR5 experimental SAS data
CORAL model
Sample: Retinoic acid receptor alpha, RAR monomer, 41 kDa Mus musculus protein
Retinoic acid receptor RXR-alpha monomer, 38 kDa Mus musculus protein
DNA response element F11r DR5 monomer, 13 kDa DNA
Buffer: 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2014 Jan 19
Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR Nucleic Acids Research (2020)
Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 130 nm3

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

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)

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

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

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