Browse by MODEL: Ab initio only

SASDB79 – Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex

Basic domain of telomeric repeat-binding factor 2telomere DNA duplex experimental SAS data
MONSA model
Sample: Basic domain of telomeric repeat-binding factor 2 monomer, 5 kDa Homo sapiens protein
Telomere DNA duplex monomer, 11 kDa DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
Necasová I, Janoušková E, Klumpler T, Hofr C
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 20 nm3

SASDB89 – Telomeric DNA duplex

telomere DNA duplex experimental SAS data
MONSA model
Sample: Telomere DNA duplex monomer, 11 kDa DNA
Buffer: 20 mM Tris-HCl, 50 mM LiCl, pH: 7.5
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2016 May 3
Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. Nucleic Acids Res 45(21):12170-12180 (2017)
Necasová I, Janoušková E, Klumpler T, Hofr C
RgGuinier 1.6 nm
Dmax 5.7 nm
VolumePorod 12 nm3

SASDCX5 – Monomeric Sortilin at pH 5.5

Sortilin 1 A464E alias Neurotensin-receptor 3 A464E experimental SAS data
DAMMIF model
Sample: Sortilin 1 A464E alias Neurotensin-receptor 3 A464E monomer, 76 kDa Mus musculus protein
Buffer: 25 mM MES pH 5.5, 150 mM NaCl, pH: 5.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Apr 17
Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release. Nat Commun 8(1):1708 (2017)
Leloup N, Lössl P, Meijer DH, Brennich M, Heck AJR, Thies-Weesie DME, Janssen BJC
RgGuinier 3.4 nm
Dmax 10.0 nm
VolumePorod 217 nm3

SASDBJ7 – Pomacea maculata perivitellin 1

Pomacea maculata perivitellin 1 experimental SAS data
DAMMIF model
Sample: Pomacea maculata perivitellin 1 dodecamer, 278 kDa Pomacea maculata protein
Buffer: 100 mM Phosphate Buffer, pH: 7.4
Experiment: SAXS data collected at SAXS2 Beamline, Brazilian Synchrotron Light Laboratory on 2015 Mar 26
Convergent evolution of plant and animal embryo defences by hyperstable non-digestible storage proteins. Sci Rep 7(1):15848 (2017)
Pasquevich MY, Dreon MS, Qiu JW, Mu H, Heras H
RgGuinier 4.2 nm
Dmax 14.3 nm
VolumePorod 537 nm3

SASDCP5 – Vaccinia virus DNA polymerase processivity factor component A20 (C-terminal fragment)

DNA polymerase processivity factor component A20 C-ter fragment experimental SAS data
DAMMIF model
Sample: DNA polymerase processivity factor component A20 C-ter fragment monomer, 17 kDa Vaccinia virus protein
Buffer: 25 mM Tris-HCl, 300 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Feb 5
The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Nat Commun 8(1):1455 (2017)
Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F
RgGuinier 2.2 nm
Dmax 7.4 nm
VolumePorod 31 nm3

SASDC82 – Rab family protein CtRoco nucleotide free

Rab family protein experimental SAS data
DAMMIN model
Sample: Rab family protein dimer, 254 kDa Chlorobaculum tepidum protein
Buffer: 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2015 Feb 16
A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover. Nat Commun 8(1):1008 (2017)
Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W
RgGuinier 5.0 nm
Dmax 18.4 nm
VolumePorod 440 nm3

SASDD53 – Tetratrico peptide repeat domain of Bacterial cellulose synthesis subunit C

Bacterial cellulose synthesis subunit C experimental SAS data
DAMMIF model
Sample: Bacterial cellulose synthesis subunit C monomer, 71 kDa Enterobacter sp. CJF-002 protein
Buffer: 50 mM HEPES, 100 mM KCl, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2017 Apr 24
Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C. Sci Rep 7(1):13018 (2017)
Nojima S, Fujishima A, Kato K, Ohuchi K, Shimizu N, Yonezawa K, Tajima K, Yao M
RgGuinier 5.1 nm
Dmax 18.5 nm
VolumePorod 115 nm3

SASDC76 – Extracellular domain of human B-lymphocyte cell receptor CD22

CD22 extracellular domain experimental SAS data
DAMMIF model
Sample: CD22 extracellular domain monomer, 90 kDa Homo sapiens protein
Buffer: 20 mM Tris 150 mM NaCl, pH: 9
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Apr 21
Molecular basis of human CD22 function and therapeutic targeting. Nat Commun 8(1):764 (2017)
Ereño-Orbea J, Sicard T, Cui H, Mazhab-Jafari MT, Benlekbir S, Guarné A, Rubinstein JL, Julien JP
RgGuinier 8.0 nm
Dmax 30.6 nm

SASDC86 – Extracellular domain of human B-lymphocyte cell receptor CD22 in complex with alpha 2,6 sialyllactose

CD22 extracellular domainalpha(2,6)-Sialyllactose experimental SAS data
DAMMIF model
Sample: CD22 extracellular domain monomer, 90 kDa Homo sapiens protein
Alpha(2,6)-Sialyllactose, 1 kDa
Buffer: 20 mM Tris 150 mM NaCl, pH: 9
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Apr 21
Molecular basis of human CD22 function and therapeutic targeting. Nat Commun 8(1):764 (2017)
Ereño-Orbea J, Sicard T, Cui H, Mazhab-Jafari MT, Benlekbir S, Guarné A, Rubinstein JL, Julien JP
RgGuinier 8.1 nm
Dmax 29.8 nm

SASDBJ9 – Geobacillus stearothermophilus DnaB1-300

Geobacillus stearothermophilus DnaB1-300 experimental SAS data
GASBOR model
Sample: Geobacillus stearothermophilus DnaB1-300 tetramer, 138 kDa Geobacillus stearothermophilus protein
Buffer: 20 mM Tris, 300 mM NaCl and 5 mM β-ME, pH: 8
Experiment: SAXS data collected at 23A, Taiwan Photon Source, NSRRC on 2015 Oct 18
Structural analyses of the bacterial primosomal protein DnaB reveal that it is a tetramer and forms a complex with a primosomal re-initiation protein. J Biol Chem 292(38):15744-15757 (2017)
Li YC, Naveen V, Lin MG, Hsiao CD
RgGuinier 3.5 nm
Dmax 11.0 nm
VolumePorod 315 nm3