Browse by MODEL: Hybrid

SASDB35 – Staphylococcus aureus thiaminase II

Thiaminase type II enzyme experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Thiaminase type II enzyme tetramer, 107 kDa Staphylococcus aureus protein
Buffer: 100 mM Tris-HCl, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 May 11
Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases. Acta Crystallogr D Biol Crystallogr 69(Pt 12):2320-9 (2013)
Begum A, Drebes J, Kikhney A, Müller IB, Perbandt M, Svergun D, Wrenger C, Betzel C
RgGuinier 3.4 nm
Dmax 11.0 nm
VolumePorod 168 nm3

SASDA45 – PpoA wild type enzyme

Psi-producing oxygenase A experimental SAS data
SASREF model
Sample: Psi-producing oxygenase A trimer, 362 kDa Aspergillus nidulans protein
Buffer: 20 Mm HEPES, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Jun 24
A structural model of PpoA derived from SAXS-analysis-implications for substrate conversion. Biochim Biophys Acta 1831(9):1449-57 (2013)
Koch C, Tria G, Fielding AJ, Brodhun F, Valerius O, Feussner K, Braus GH, Svergun DI, Bennati M, Feussner I
RgGuinier 5.4 nm
Dmax 16.5 nm
VolumePorod 540 nm3

SASDAV5 – apo XMRV RT

apo XMRV RT experimental SAS data
CRYSOL model
Sample: Apo XMRV RT monomer, 75 kDa Escherichia coli protein
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 4.0 nm
Dmax 13.5 nm
VolumePorod 160 nm3

SASDAW5 – XMRV RT + DNA/RNA hybrid

apo XMRV RTRNA_DNA hybrid substrate experimental SAS data
CRYSOL model
Sample: Apo XMRV RT monomer, 75 kDa Escherichia coli protein
RNA_DNA hybrid substrate monomer, 15 kDa
Buffer: 10 mM HEPES 100 mM KCl 5% Glycerol, pH: 6.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2011 Dec 8
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874-87 (2013)
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M
RgGuinier 3.5 nm
Dmax 11.5 nm
VolumePorod 155 nm3

SASDL47 – Oligomeric composition of AXH Domain of Ataxin-1 (wild type and A567G, I580A mutants)

Ataxin-1 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Ataxin-1 monomer, 14 kDa Homo sapiens protein
Buffer: 20 mM Tris-HCl, pH: 7
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Oct 21
Self-assembly and conformational heterogeneity of the AXH domain of ataxin-1: an unusual example of a chameleon fold. Biophys J 104(6):1304-13 (2013)
de Chiara C, Rees M, Menon RP, Pauwels K, Lawrence C, Konarev PV, Svergun DI, Martin SR, Chen YW, Pastore A
RgGuinier 5.5 nm

SASDDJ2 – Calcium-bound polcalcin Phl p 7

polcalcin Phl p 7 experimental SAS data
MES-FOXS model
Sample: Polcalcin Phl p 7 monomer, 9 kDa Phleum pratense protein
Buffer: 0.15M NaCl, 0.025M Hepes, pH 7.4, 100 uM Ca2+, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2011 Dec 8
Solution structures of polcalcin Phl p 7 in three ligation states: Apo-, hemi-Mg2+-bound, and fully Ca2+-bound. Proteins 81(2):300-15 (2013)
Henzl MT, Sirianni AG, Wycoff WG, Tan A, Tanner JJ
RgGuinier 1.3 nm
Dmax 3.6 nm
VolumePorod 14 nm3

SASDHY2 – Human APPL2 (DCC-interacting protein 13-beta)

Adaptor protein, phosphotyrosine interaction, pleckstrin homology domain, and leucine zipper-containing protein 2 experimental SAS data
BUNCH model
Sample: Adaptor protein, phosphotyrosine interaction, pleckstrin homology domain, and leucine zipper-containing protein 2 dimer, 87 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 8.5
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 7 Apr 20
Membrane curvature protein exhibits interdomain flexibility and binds a small GTPase. J Biol Chem 287(49):40996-1006 (2012)
King GJ, Stöckli J, Hu SH, Winnen B, Duprez WG, Meoli CC, Junutula JR, Jarrott RJ, James DE, Whitten AE, Martin JL
RgGuinier 5.1 nm
Dmax 18.0 nm
VolumePorod 140 nm3

SASDAT4 – uPAR wild-type

Urokinase plasminogen activator surface receptor experimental SAS data
DAMMIF model
Sample: Urokinase plasminogen activator surface receptor monomer, 37 kDa Homo sapiens protein
Buffer: 25 mM Sodium Phosphate 5 % Glycerol 50 mM NaSO4, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Jun 10
A flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR). J Biol Chem 287(41):34304-15 (2012)
Mertens HD, Kjaergaard M, Mysling S, Gårdsvoll H, Jørgensen TJ, Svergun DI, Ploug M
RgGuinier 2.8 nm
Dmax 9.7 nm
VolumePorod 69 nm3

SASDAU4 – uPAR H47C/N259C

Urokinase plasminogen activator surface receptor experimental SAS data
DAMMIF model
Sample: Urokinase plasminogen activator surface receptor monomer, 37 kDa Homo sapiens protein
Buffer: 25 mM Sodium Phosphate 5 % Glycerol 50 mM NaSO4, pH: 7.2
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Jun 10
A flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR). J Biol Chem 287(41):34304-15 (2012)
Mertens HD, Kjaergaard M, Mysling S, Gårdsvoll H, Jørgensen TJ, Svergun DI, Ploug M
RgGuinier 2.2 nm
Dmax 7.0 nm
VolumePorod 57 nm3

SASDAH5 – Complex of Hfq with DsrA

RNA chaperone HfqRNA DsrA experimental SAS data
SASREF model
Sample: RNA chaperone Hfq hexamer, 67 kDa Escherichia coli protein
RNA DsrA monomer, 12 kDa RNA
Buffer: 50 mM Tris-HCL 150 mM NaCl 1.0 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL X33, DORIS III, DESY on 2010 Nov 16
Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res 40(16):8072-84 (2012)
Ribeiro Ede A Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K
RgGuinier 4.3 nm
Dmax 14.5 nm
VolumePorod 210 nm3