Browse by MODEL: Ab initio only

SASDFG6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex

Beta sliding clampProbable exodeoxyribonuclease III protein XthADNA ligase A experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 5.8 nm
Dmax 25.3 nm
VolumePorod 501 nm3

SASDFH6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex in the presence of DNA substrate

Probable exodeoxyribonuclease III protein XthADNA ligase ABeta sliding clampDNA ligase A nicked DNA substrate experimental SAS data
DAMMIF model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
DNA ligase A nicked DNA substrate dimer, 16 kDa DNA
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 5.8 nm
Dmax 19.1 nm
VolumePorod 496 nm3

SASDQG6 – N-terminal truncation mutant of the periplasmic region of conjugal transfer mating pair stabilization protein TraG* from the R100 plasmid

Conjugal transfer mating pair stabilization protein TraG experimental SAS data
DAMMIF model
Sample: Conjugal transfer mating pair stabilization protein TraG monomer, 52 kDa Shigella flexneri 4c protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5% glycerol, pH: 7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 23
Solution characterization of the dynamic conjugative entry exclusion protein TraG Structural Dynamics 9(6):064702 (2022)
Bragagnolo N, Audette G
RgGuinier 4.1 nm
Dmax 17.5 nm
VolumePorod 130 nm3

SASDQH6 – Periplasmic region of the conjugal transfer mating pair stabilization protein TraG* from the R100 plasmid

Conjugal transfer mating pair stabilization protein TraG experimental SAS data
DAMMIF model
Sample: Conjugal transfer mating pair stabilization protein TraG monomer, 57 kDa Shigella flexneri 4c protein
Buffer: 20 mM HEPES, 100 mM NaCl, 5% glycerol, 0.05% NP40, pH: 7
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2022 Feb 23
Solution characterization of the dynamic conjugative entry exclusion protein TraG Structural Dynamics 9(6):064702 (2022)
Bragagnolo N, Audette G
RgGuinier 5.8 nm
Dmax 45.0 nm

SASDQQ5 – Oligomerisation domain of phosphoprotein from Borna disease virus

Phosphoprotein experimental SAS data
DAMMIF model
Sample: Phosphoprotein tetramer, 47 kDa Borna disease virus … protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5 mM β- mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Sep 1
Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing. Viruses 14(11) (2022)
Tarbouriech N, Chenavier F, Kawasaki J, Bachiri K, Bourhis JM, Legrand P, Freslon LL, Laurent EMN, Suberbielle E, Ruigrok RWH, Tomonaga K, Gonzalez-Dunia D, Horie M, Coyaud E, Crépin T
RgGuinier 4.5 nm
Dmax 17.0 nm
VolumePorod 66 nm3

SASDQR5 – Oligomerisation domain of phosphoprotein from Munia bornavirus

Phosphoprotein oligomerisation domain experimental SAS data
DAMMIF model
Sample: Phosphoprotein oligomerisation domain tetramer, 50 kDa protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5 mM β- mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Sep 1
Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing. Viruses 14(11) (2022)
Tarbouriech N, Chenavier F, Kawasaki J, Bachiri K, Bourhis JM, Legrand P, Freslon LL, Laurent EMN, Suberbielle E, Ruigrok RWH, Tomonaga K, Gonzalez-Dunia D, Horie M, Coyaud E, Crépin T
RgGuinier 4.6 nm
Dmax 17.8 nm
VolumePorod 70 nm3

SASDQS5 – Oligomerisation domain of phosphoprotein from Gaboon viper virus

Phosphoprotein experimental SAS data
DAMMIF model
Sample: Phosphoprotein tetramer, 52 kDa Gaboon viper virus … protein
Buffer: 20 mM HEPES, 150 mM NaCl, 5 mM β- mercaptoethanol, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Sep 1
Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing. Viruses 14(11) (2022)
Tarbouriech N, Chenavier F, Kawasaki J, Bachiri K, Bourhis JM, Legrand P, Freslon LL, Laurent EMN, Suberbielle E, Ruigrok RWH, Tomonaga K, Gonzalez-Dunia D, Horie M, Coyaud E, Crépin T
RgGuinier 4.6 nm
Dmax 17.5 nm
VolumePorod 75 nm3

SASDNF2 – Serine/threonine-protein phosphatase (PP1) bound to Protein phosphatase 1 (PTG)

Serine/threonine-protein phosphatase PP1-alpha catalytic subunitProtein phosphatase 1 regulatory subunit 3C experimental SAS data
DAMMIF model
Sample: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit monomer, 37 kDa Homo sapiens protein
Protein phosphatase 1 regulatory subunit 3C monomer, 23 kDa Homo sapiens protein
Buffer: 50 mM Tris pH 8.0, 0.5 M NaCl, 10% glycerol, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 7
Molecular architecture of the glycogen- committed PP1/PTG holoenzyme. Nat Commun 13(1):6199 (2022)
Semrau MS, Giachin G, Covaceuszach S, Cassetta A, Demitri N, Storici P, Lolli G
RgGuinier 3.3 nm
Dmax 11.9 nm
VolumePorod 87 nm3

SASDNG2 – Serine/threonine-protein phosphatase (PP1) bound to Protein phosphatase 1 (PTG) and cyclodextrin

Serine/threonine-protein phosphatase PP1-alpha catalytic subunitProtein phosphatase 1 regulatory subunit 3C experimental SAS data
DAMFILT model
Sample: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit monomer, 37 kDa Homo sapiens protein
Protein phosphatase 1 regulatory subunit 3C monomer, 23 kDa Homo sapiens protein
Buffer: 50 mM Tris pH 8.0, 0.5 M NaCl, 10% glycerol, 1 mM DTT, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 7
Molecular architecture of the glycogen- committed PP1/PTG holoenzyme. Nat Commun 13(1):6199 (2022)
Semrau MS, Giachin G, Covaceuszach S, Cassetta A, Demitri N, Storici P, Lolli G
RgGuinier 3.6 nm
Dmax 12.3 nm
VolumePorod 89 nm3

SASDNH2 – Complex of Geobacter sulfurreducens pAgo with Sir2-like effector protein

Piwi domain proteinSir2 superfamily protein experimental SAS data
GASBOR model
Sample: Piwi domain protein monomer, 53 kDa Geobacter sulfurreducens (strain … protein
Sir2 superfamily protein monomer, 68 kDa Geobacter sulfurreducens (strain … protein
Buffer: 20 mM TrisHCl, pH 7.5, 5 mM MgCl2, 150 mM NaCl and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 27
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion Nature Microbiology (2022)
Zaremba M, Dakineviciene D, Golovinas E, Zagorskaitė E, Stankunas E, Lopatina A, Sorek R, Manakova E, Ruksenaite A, Silanskas A, Asmontas S, Grybauskas A, Tylenyte U, Jurgelaitis E, Grigaitis R, Timinskas K, Venclovas Č, Siksnys V
RgGuinier 3.6 nm
Dmax 11.4 nm
VolumePorod 185 nm3