Browse by MODEL: Ab initio only

SASDED6 – Proliferating cell nuclear antigen - UbPCNA - Split Fusion Trimer

Proliferating cell nuclear antigen experimental SAS data
UIOWA_BD model
Sample: Proliferating cell nuclear antigen trimer, 117 kDa Saccharomyces cerevisiae protein
Buffer: 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2018 Aug 6
Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods. J Mol Biol 430(24):5294-5303 (2018)
Powers KT, Lavering ED, Washington MT
RgGuinier 4.1 nm
Dmax 14.0 nm
VolumePorod 238 nm3

SASDEE6 – Proliferating cell nuclear antigen - SUMOPCNA - Split Fusion Trimer

Proliferating cell nuclear antigen experimental SAS data
UIOWA_BD model
Sample: Proliferating cell nuclear antigen trimer, 125 kDa Saccharomyces cerevisiae protein
Buffer: 20 mM Tris, 150 mM NaCl, 5% glycerol, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2018 Aug 6
Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods. J Mol Biol 430(24):5294-5303 (2018)
Powers KT, Lavering ED, Washington MT
RgGuinier 4.7 nm
Dmax 16.9 nm
VolumePorod 310 nm3

SASDET5 – Old Yellow Enzyme of Leishmania braziliensis

Old Yellow Enzyme of Leishmania braziliensis experimental SAS data
DAMMIN model
Sample: Old Yellow Enzyme of Leishmania braziliensis monomer, 42 kDa Leishmania braziliensis protein
Buffer: 25 mM Tris-HCl 100 mM NaCl and 1 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at SAXS1 Beamline, Brazilian Synchrotron Light Laboratory on 2015 May 26
Structural studies of Old Yellow Enzyme of Leishmania braziliensis in solution. Arch Biochem Biophys (2018)
Walbert Veloso-Silva LL, Dores-Silva PR, Bertolino Reis DE, Moreno Oliveira LF, Libardi SH, Borges JC
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 73 nm3

SASDED8 – Poly-L-Glutamic Acid in Dimethyl Sulfoxide (DMSO)

Poly-L-Glutamic Acid experimental SAS data
PYMOL model
Sample: Poly-L-Glutamic Acid, 6 kDa
Buffer: Dimethyl Sulfoxide (DMSO), pH:
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Dec 11
β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 122(50):11895-11905 (2018)
Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W
RgGuinier 1.8 nm
Dmax 7.8 nm
VolumePorod 5 nm3

SASDEF6 – Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455)

Epstein-Barr nuclear antigen 2 experimental SAS data
DAMMIN model
Sample: Epstein-Barr nuclear antigen 2 dimer, 16 kDa Human gammaherpesvirus 4 protein
Buffer: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Sep 23
Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth (2018)
Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M
RgGuinier 2.7 nm
Dmax 9.3 nm
VolumePorod 19 nm3

SASDEG6 – Epstein-Barr nuclear antigen 2 (EBNA2 Type2, amino acids 348-422)

Epstein-Barr nuclear antigen 2 experimental SAS data
DAMMIN model
Sample: Epstein-Barr nuclear antigen 2 dimer, 16 kDa Human gammaherpesvirus 4 protein
Buffer: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Sep 23
Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth (2018)
Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M
RgGuinier 2.8 nm
Dmax 10.4 nm
VolumePorod 20 nm3

SASDEH6 – BS69 (CC-MYND: Zinc finger MYND domain-containing protein 11, amino acids 480-602)

Zinc finger MYND domain-containing protein 11 experimental SAS data
DAMMIN model
Sample: Zinc finger MYND domain-containing protein 11 tetramer, 60 kDa Homo sapiens protein
Buffer: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Sep 23
Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth (2018)
Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M
RgGuinier 5.3 nm
Dmax 16.9 nm
VolumePorod 83 nm3

SASDEJ6 – Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)

Epstein-Barr nuclear antigen 2Zinc finger MYND domain-containing protein 11 experimental SAS data
DAMMIN model
Sample: Epstein-Barr nuclear antigen 2 dimer, 16 kDa Human gammaherpesvirus 4 protein
Zinc finger MYND domain-containing protein 11 tetramer, 60 kDa Homo sapiens protein
Buffer: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Nov 29
Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth (2018)
Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M
RgGuinier 4.6 nm
Dmax 13.8 nm
VolumePorod 72 nm3

SASDEK6 – Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type2, amino acids 348-422) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)

Epstein-Barr nuclear antigen 2Zinc finger MYND domain-containing protein 11 experimental SAS data
DAMMIN model
Sample: Epstein-Barr nuclear antigen 2 dimer, 16 kDa Human gammaherpesvirus 4 protein
Zinc finger MYND domain-containing protein 11 hexamer, 90 kDa Homo sapiens protein
Buffer: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Sep 23
Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth (2018)
Ponnusamy R, Khatri R, Correia P, Mancini E, Farrell P, West M
RgGuinier 4.7 nm
Dmax 14.5 nm
VolumePorod 239 nm3

SASDD32 – DNA-(adenine N6)-methyltransferase from Acinetobacter baumannii ATCC 17978

DNA-(adenine N6)-methyltransferase experimental SAS data
DAMMIN model
Sample: DNA-(adenine N6)-methyltransferase monomer, 49 kDa Acinetobacter baumannii protein
Buffer: 150mM NaCl, 10mM Tris, 1mM DTT, 5% v/v glycerol, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 30
Recombinant production of A1S_0222 from Acinetobacter baumannii ATCC 17978 and confirmation of its DNA-(adenine N6)-methyltransferase activity. Protein Expr Purif 151:78-85 (2018)
Blaschke U, Suwono B, Zafari S, Ebersberger I, Skiebe E, Jeffries CM, Svergun DI, Wilharm G
RgGuinier 2.9 nm
Dmax 11.1 nm
VolumePorod 96 nm3