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12 hits found for Yadav

SASDPY2 – SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein monomer

Replicase polyprotein 1ab experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1ab monomer, 31 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 500 mM NaCl, 5% glycerol, and 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Oct 15
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 2.5 nm
Dmax 8.8 nm
VolumePorod 50 nm3

SASDPZ2 – SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein dimer

Replicase polyprotein 1ab experimental SAS data
Replicase polyprotein 1ab Kratky plot
Sample: Replicase polyprotein 1ab dimer, 63 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 500 mM NaCl, 5% glycerol, and 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Oct 15
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 3.3 nm
Dmax 11.8 nm
VolumePorod 110 nm3

SASDP23 – SARS-CoV-2 non-structural protein 7-11 (nsp7-11) polyprotein monomer

Replicase polyprotein 1a experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1a monomer, 60 kDa Severe acute respiratory … protein
Buffer: 20 mM HEPES, 10% glycerol, 500 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Nov 14
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 3.5 nm
Dmax 15.6 nm
VolumePorod 102 nm3

SASDP33 – SARS-CoV-2 non-structural protein 7-11 (nsp7-11) polyprotein dimer

Replicase polyprotein 1a experimental SAS data
Replicase polyprotein 1a Kratky plot
Sample: Replicase polyprotein 1a dimer, 119 kDa Severe acute respiratory … protein
Buffer: 20 mM HEPES, 10% glycerol, 500 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Nov 14
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 4.6 nm
Dmax 19.1 nm
VolumePorod 203 nm3

SASDGX4 – Aryl-hydrocarbon-interacting protein-like 1

Aryl-hydrocarbon-interacting protein-like 1(1-316) experimental SAS data
Aryl-hydrocarbon-interacting protein-like 1(1-316) Kratky plot
Sample: Aryl-hydrocarbon-interacting protein-like 1(1-316) monomer, 37 kDa Homo sapiens protein
Buffer: 50 mM Tris, 100 mM NaCl, 2.5 % glycerol and 6 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2018 Jul 17
Interaction of the tetratricopeptide repeat domain of aryl hydrocarbon receptor-interacting protein-like 1 with the regulatory Pγ subunit of phosphodiesterase 6. J Biol Chem 294(43):15795-15807 (2019)
Yadav RP, Boyd K, Yu L, Artemyev NO
RgGuinier 2.6 nm
Dmax 9.1 nm
VolumePorod 60 nm3

SASDJ95 – E3 ubiquitin-protein ligase BRE1 complexed with E2 ubiquitin conjugating enzyme RAD6

E3 ubiquitin-protein ligase BRE1Ubiquitin-conjugating enzyme E2 2 experimental SAS data
SREFLEX model
Sample: E3 ubiquitin-protein ligase BRE1 dimer, 50 kDa Saccharomyces cerevisiae (strain … protein
Ubiquitin-conjugating enzyme E2 2 monomer, 20 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Feb 11
Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones International Journal of Biological Macromolecules :127717 (2023)
Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa S, Kamthan M, Kumar P
RgGuinier 4.1 nm
Dmax 10.4 nm
VolumePorod 105 nm3

SASDJA5 – E2 ubiquitin conjugating enzyme RAD6

Ubiquitin-conjugating enzyme E2 2 experimental SAS data
SREFLEX model
Sample: Ubiquitin-conjugating enzyme E2 2 monomer, 20 kDa Saccharomyces cerevisiae (strain … protein
Buffer: 50 mM Tris, 150 mM NaCl, 1 mM TCEP, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Feb 11
Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones International Journal of Biological Macromolecules :127717 (2023)
Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa S, Kamthan M, Kumar P
RgGuinier 2.3 nm
Dmax 6.6 nm
VolumePorod 31 nm3

SASDSY8 – S9C peptidase from Geobacillus stearothermophilus

Acylamino-acid-releasing enzyme (I277L, V491A) experimental SAS data
GASBOR model
Sample: Acylamino-acid-releasing enzyme (I277L, V491A) tetramer, 308 kDa Geobacillus stearothermophilus protein
Buffer: 10 mM Tris, 100 mM NaCl, pH: 8
Experiment: SAXS data collected at BL-18, INDUS-2 on 2023 Aug 11
Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Lett (2024)
...Yadav P, Kumar A, Makde RD
RgGuinier 5.3 nm
Dmax 13.0 nm
VolumePorod 424 nm3

SASDF29 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4ADP-ribosylation factor1 - short experimental SAS data
OTHER model
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 4 monomer, 8 kDa Homo sapiens protein
ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2015 Dec 10
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 1.7 nm
Dmax 6.0 nm
VolumePorod 21 nm3

SASDF39 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

ADP-ribosylation factor1 - shortDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 experimental SAS data
OTHER model
Sample: ADP-ribosylation factor1 - short monomer, 11 kDa Homo sapiens RNA
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
Buffer: 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH: 8
Experiment: SAXS data collected at Rigaku BioSAXS-1000, CEITEC on 2018 May 29
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.1 nm
Dmax 6.4 nm
VolumePorod 39 nm3

SASDF49 – Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 - long

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4ADP-ribosylation factor1 - long experimental SAS data
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 ADP-ribosylation factor1 - long Kratky plot
Sample: Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 monomer, 20 kDa Homo sapiens protein
ADP-ribosylation factor1 - long monomer, 16 kDa Homo sapiens RNA
Buffer: 50 mM potassium phosphate, 100 mM NaCl, 3.5 mM 2-mercaptoethanol, pH: 6.8
Experiment: SAXS data collected at B21, Diamond Light Source on 2018 Sep 20
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Res (2019)
Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
RgGuinier 2.5 nm
Dmax 7.0 nm
VolumePorod 53 nm3

SASDPB9 – SAXS analysis of pilus adhesin PitA from pilus islet-2 of Streptococcus oralis

von Willebrand factor type A domain protein experimental SAS data
MODELLER model
Sample: von Willebrand factor type A domain protein monomer, 89 kDa Streptococcus oralis ATCC … protein
Buffer: 20 mM HEPES,150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2017 May 12
New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer. FEBS J (2022)
Yadav RK, Krishnan V
RgGuinier 6.4 nm
Dmax 29.2 nm
VolumePorod 217 nm3