Browse by MODEL: Ab initio only

SASDMS2 – HPMA-Based Nanoparticles with Cholesterol (2.7%)

N-(2-hydroxypropyl)- 31 methacrylamide (HPMA) copolymers with Cholesterol (2.7%) experimental SAS data
DAMFILT model
Sample: N-(2-hydroxypropyl)- 31 methacrylamide (HPMA) copolymers with Cholesterol (2.7%) 0, 16740 kDa
Buffer: phosphate buffer saline (PBS) (pH 7.2), pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Mar 27
Macromolecular HPMA-based nanoparticles with cholesterol for solid-tumor targeting: detailed study of the inner structure of a highly efficient drug delivery system. Biomacromolecules 13(8):2594-604 (2012)
Filippov SK, Chytil P, Konarev PV, Dyakonova M, Papadakis C, Zhigunov A, Plestil J, Stepanek P, Etrych T, Ulbrich K, Svergun DI
RgGuinier 5.2 nm
Dmax 28.1 nm

SASDMT2 – HPMA-Based Nanoparticles with Cholesterol (3.0%)

N-(2-hydroxypropyl)- 31 methacrylamide (HPMA) copolymers with Cholesterol (3.0%) experimental SAS data
DAMFILT model
Sample: N-(2-hydroxypropyl)- 31 methacrylamide (HPMA) copolymers with Cholesterol (3.0%) 0, 29520 kDa
Buffer: phosphate buffer saline (PBS) (pH 5.0), pH: 5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Mar 27
Macromolecular HPMA-based nanoparticles with cholesterol for solid-tumor targeting: detailed study of the inner structure of a highly efficient drug delivery system. Biomacromolecules 13(8):2594-604 (2012)
Filippov SK, Chytil P, Konarev PV, Dyakonova M, Papadakis C, Zhigunov A, Plestil J, Stepanek P, Etrych T, Ulbrich K, Svergun DI
RgGuinier 9.4 nm
Dmax 43.2 nm

SASDMM9 – Response Regulator RocR from Pseudomonas aeruginosa

RocR experimental SAS data
OTHER model
Sample: RocR tetramer, 171 kDa Pseudomonas aeruginosa (strain … protein
Buffer: 50 mM Tris–HCl, 250 mM NaCl, 10 mM imidazole, 5% glycerol, 0.5 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 9
Structural Insights into the Regulatory Mechanism of the Response Regulator RocR from Pseudomonas aeruginosa in Cyclic Di-GMP Signaling Journal of Bacteriology 194(18):4837-4846 (2012)
Chen M, Kotaka M, Vonrhein C, Bricogne G, Rao F, Chuah M, Svergun D, Schneider G, Liang Z, Lescar J
RgGuinier 3.7 nm
Dmax 11.0 nm

SASDLV5 – Myosin Filament-Linking Protein Myomesin-1 (domains My9-My13, dimer)

Myomesin-1 experimental SAS data
DAMMIN model
Sample: Myomesin-1 dimer, 121 kDa Homo sapiens protein
Buffer: 25 mMTris-HCl, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 May 10
Superhelical architecture of the myosin filament-linking protein myomesin with unusual elastic properties. PLoS Biol 10(2):e1001261 (2012)
Pinotsis N, Chatziefthimiou SD, Berkemeier F, Beuron F, Mavridis IM, Konarev PV, Svergun DI, Morris E, Rief M, Wilmanns M
RgGuinier 9.6 nm
Dmax 37.0 nm

SASDAS6 – Plectin, fragment of the plakin domain encompassing the spectrin repeats SR3-SR4-SR5 and the SH3

Plectin experimental SAS data
DAMMIF model
Sample: Plectin monomer, 43 kDa Homo sapiens protein
Buffer: 20 mM Sodium Phosphate 150 mM NaCl 5% glycerol 2.5 mM DTT, pH: 7.5
Experiment: SAXS data collected at cSAXS, Swiss Light Source on 2009 Jul 24
The structure of the plakin domain of plectin reveals a non-canonical SH3 domain interacting with its fourth spectrin repeat. J Biol Chem 286(14):12429-38 (2011)
Ortega E, Buey RM, Sonnenberg A, de Pereda JM
RgGuinier 4.4 nm
Dmax 14.5 nm
VolumePorod 57 nm3

SASDLR5 – Multidomain Regulatory Protein Rv1364c (monomer)

Multidomain regulatory protein Rv1364c experimental SAS data
GASBOR model
Sample: Multidomain regulatory protein Rv1364c monomer, 70 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 25 mM Tris-HCl, 50 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2007 Feb 14
Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis. Structure 19(1):56-69 (2011)
King-Scott J, Konarev PV, Panjikar S, Jordanova R, Svergun DI, Tucker PA
RgGuinier 3.8 nm
Dmax 14.0 nm
VolumePorod 130 nm3

SASDLS5 – Multidomain Regulatory Protein Rv1364c (dimer)

Multidomain regulatory protein Rv1364c experimental SAS data
GASBOR model
Sample: Multidomain regulatory protein Rv1364c dimer, 139 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 25 mM Tris-HCl, 50 mM NaCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2007 Feb 14
Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis. Structure 19(1):56-69 (2011)
King-Scott J, Konarev PV, Panjikar S, Jordanova R, Svergun DI, Tucker PA
RgGuinier 4.5 nm
Dmax 18.0 nm
VolumePorod 289 nm3

SASDLF3 – Staphylococcal immunoglobulin-binding protein bound to complement component C3

Protein A experimental SAS data
DAMMIN model
Sample: Protein A monomer, 28 kDa Staphylococcus aureus protein
Buffer: 10 mM HEPES, pH 7.2, 3 mM EDTA, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2005 May 12
A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d Molecular Immunology 48(4):452-462 (2011)
Clark E, Crennell S, Upadhyay A, Zozulya A, Mackay J, Svergun D, Bagby S, van den Elsen J
RgGuinier 4.6 nm
Dmax 16.0 nm
VolumePorod 81 nm3

SASDC66 – Blue light receptor YtvA, lit/active state

pfyP - Blue light photoreceptor experimental SAS data
GASBOR model
Sample: PfyP - Blue light photoreceptor dimer, 58 kDa Bacillus subtilis protein
Buffer: PBS + 5 mM DTT, pH: 7.4
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2009 Oct 24
The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study. J Mol Biol 403(1):78-87 (2010)
Jurk M, Dorn M, Kikhney A, Svergun D, Gärtner W, Schmieder P
RgGuinier 3.2 nm
Dmax 10.1 nm
VolumePorod 74 nm3

SASDMN9 – Conformational characterization of A77-78 fibronectin type III tandem

Titin experimental SAS data
OTHER model
Sample: Titin monomer, 22 kDa Homo sapiens protein
Buffer: 100 mM NaCl, 50 mM Tris-HCl, 2mM DTT, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2006 Jul 3
The Structure of the FnIII Tandem A77-A78 Points to a Periodically Conserved Architecture in the Myosin-Binding Region of Titin Journal of Molecular Biology 401(5):843-853 (2010)
Bucher R, Svergun D, Muhle-Goll C, Mayans O
RgGuinier 2.5 nm
Dmax 90.0 nm
VolumePorod 21 nm3