Browse by MODEL: Ab initio only

SASDDK9 – Conformation of R1-3 human dystrophin fragment in interaction with zwitterionic phospholipid bicelles (SANS)

R1-3 human dystrophin fragment experimental SAS data
DAMMIF model
Sample: R1-3 human dystrophin fragment monomer, 39 kDa Homo sapiens protein
Buffer: 20 mM Tris-d11, 150 mM NaCl, 0.1 mM EDTA-d16, in 100% D2O, pD 7.5, pH: 7.1
Experiment: SANS data collected at D22, Institut Laue-Langevin (ILL) on 2016 Nov 7
Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids. Biophys J 115(7):1231-1239 (2018)
Dos Santos Morais R, Delalande O, Pérez J, Mias-Lucquin D, Lagarrigue M, Martel A, Molza AE, Chéron A, Raguénès-Nicol C, Chenuel T, Bondon A, Appavou MS, Le Rumeur E, Combet S, Hubert JF
RgGuinier 4.1 nm
Dmax 17.8 nm
VolumePorod 50 nm3

SASDDZ8 – Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)

Fusion protein of LSm and MyoX-coil experimental SAS data
DAMMIN model
Sample: Fusion protein of LSm and MyoX-coil, 1066 kDa Artificial protein protein
Buffer: 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol, pH: 8
Experiment: SAXS data collected at BL-6A, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2017 Nov 11
Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew Chem Int Ed Engl (2018)
Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K
RgGuinier 9.4 nm
Dmax 23.0 nm

SASDDY8 – Chicken ovalbumin gel at high pH

Ovalbumin experimental SAS data
DAMMIF model
Sample: Ovalbumin monomer, 43 kDa Gallus gallus protein
Buffer: 0.16 M NaOH, pH: 13.2
Experiment: SAXS data collected at X9A, National Synchrotron Light Source (NSLS) on 2014 Feb 21
The Proof Is in the Pidan: Generalizing Proteins as Patchy Particles. ACS Cent Sci 4(7):840-853 (2018)
Cai J, Sweeney AM

SASDB75 – Escherichia coli TraE protein: A VirB8 homolog from plasmid pKM101

Escherichia coli TraE protein (VirB8 homolog) experimental SAS data
GASBOR model
Sample: Escherichia coli TraE protein (VirB8 homolog) hexamer, 171 kDa Escherichia coli protein
Buffer: 50 mM sodium phosphate 300 mM NaCl 40 mM imidazole 0.15 % octyl glucose neopentyl glycol (OGNG), pH: 7.4
Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2016 Jun 2
VirB8 homolog TraE from plasmid pKM101 forms a hexameric ring structure and interacts with the VirB6 homolog TraD. Proc Natl Acad Sci U S A 115(23):5950-5955 (2018)
Casu B, Mary C, Sverzhinsky A, Fouillen A, Nanci A, Baron C
RgGuinier 4.4 nm
Dmax 13.7 nm
VolumePorod 360 nm3

SASDCC8 – Human TERC 1-20 DNA G-quadruplex

Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 experimental SAS data
DAMMIN model
Sample: Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 dimer, 13 kDa Homo sapiens DNA
Buffer: 20 mM HEPES, 100 mM KCl,, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Aug 2
Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. Nucleic Acids Res 46(10):5319-5331 (2018)
Meier M, Moya-Torres A, Krahn NJ, McDougall MD, Orriss GL, McRae EKS, Booy EP, McEleney K, Patel TR, McKenna SA, Stetefeld J
RgGuinier 1.4 nm
Dmax 4.6 nm
VolumePorod 15 nm3

SASDDS4 – cGMP-dependent protein kinase 1: ∆53 PKG Iα

cGMP-dependent protein kinase 1 experimental SAS data
DAMFILT model
Sample: CGMP-dependent protein kinase 1 monomer, 70 kDa Bos taurus protein
Buffer: 50 mM MES, 300 mM NaCl, 1 mM TCEP, 5 mM DTT, pH: 6.9
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2015 Jun 6
An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation. J Biol Chem 293(21):7916-7929 (2018)
Moon TM, Sheehe JL, Nukareddy P, Nausch LW, Wohlfahrt J, Matthews DE, Blumenthal DK, Dostmann WR
RgGuinier 3.0 nm
Dmax 9.7 nm
VolumePorod 105 nm3

SASDC95 – Light encoded DNA biosensor: e14A DNA

e14A experimental SAS data
DAMMIF model
Sample: E14A monomer, 21 kDa DNA
Buffer: 154 mM NaCl, pH: 8.3
Experiment: SAXS data collected at BM29, ESRF on 2016 Jun 16
Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 13(5):1235-1242 (2018)
Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV
RgGuinier 2.8 nm
Dmax 12.5 nm

SASDCA5 – Light encoded DNA biosensor: e14B DNA

e14B experimental SAS data
DAMMIF model
Sample: E14B monomer, 13 kDa DNA
Buffer: 154 mM NaCl, pH: 8.3
Experiment: SAXS data collected at BM29, ESRF on 2016 Jun 16
Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 13(5):1235-1242 (2018)
Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV
RgGuinier 1.9 nm
Dmax 9.0 nm

SASDCB5 – Light encoded DNA biosensor: e14C DNA

e14C experimental SAS data
DAMFILT model
Sample: E14C monomer, 5 kDa DNA
Buffer: 154 mM NaCl, pH: 8.3
Experiment: SAXS data collected at BM29, ESRF on 2016 Jun 16
Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 13(5):1235-1242 (2018)
Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV
RgGuinier 1.3 nm
Dmax 5.0 nm

SASDCC5 – Light encoded DNA biosensor: e14AB DNA

e14AB experimental SAS data
DAMFILT model
Sample: E14AB monomer, 93 kDa DNA
Buffer: 154 mM NaCl, pH: 8.3
Experiment: SAXS data collected at BM29, ESRF on 2016 Jun 16
Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 13(5):1235-1242 (2018)
Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV
RgGuinier 5.4 nm
Dmax 24.7 nm