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15 hits found for Manakova

SASDJB2 – Restriction endonuclease R.AgeI in apo form, monomeric

Type-2 restriction enzyme AgeI experimental SAS data
DAMMIN model
Sample: Type-2 restriction enzyme AgeI monomer, 31 kDa Thalassobius gelatinovorus protein
Buffer: 10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM CaCl₂, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 14
Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 45(6):3547-3558 (2017)
...Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V
RgGuinier 2.2 nm
Dmax 6.7 nm
VolumePorod 53 nm3

SASDJC2 – Restriction endonuclease R.AgeI complex with cognate DNA

Type-2 restriction enzyme AgeICognate DNA oligoduplex with 5'-T overhang experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Type-2 restriction enzyme AgeI dimer, 61 kDa Thalassobius gelatinovorus protein
Cognate DNA oligoduplex with 5'-T overhang dimer, 8 kDa DNA
Buffer: 10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM CaCl₂, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Nov 14
Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 45(6):3547-3558 (2017)
...Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V
RgGuinier 2.4 nm
Dmax 7.4 nm
VolumePorod 69 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)
...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

SASDJW2 – Modification dependent EcoKMcrA restriction endonuclease

5-methylcytosine-specific restriction enzyme A experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: 5-methylcytosine-specific restriction enzyme A dimer, 65 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
...Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 3.7 nm
Dmax 13.0 nm
VolumePorod 95 nm3

SASDJX2 – Modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

cognate hemimethylated 12-bp oligoduplex5-methylcytosine-specific restriction enzyme A experimental SAS data
SASREF model
Sample: cognate hemimethylated 12-bp oligoduplex dimer, 15 kDa DNA
5-methylcytosine-specific restriction enzyme A dimer, 65 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
...Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 3.9 nm
Dmax 13.5 nm
VolumePorod 69 nm3

SASDJY2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease

5-methylcytosine-specific restriction enzyme A (N-terminal domain) experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
...Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3

SASDJZ2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

5-methylcytosine-specific restriction enzyme A (N-terminal domain)cognate hemimethylated 12-bp oligoduplex experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
cognate hemimethylated 12-bp oligoduplex monomer, 7 kDa DNA
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
...Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3

SASDPC4 – Complex of Rhodopseudomonas palustris pAgo with TIR-like effector protein

TIR domain-containing proteinUncharacterized protein (PIWI) experimental SAS data
ALPHAFOLD model
Sample: TIR domain-containing protein monomer, 57 kDa Rhodopseudomonas palustris (strain … protein
Uncharacterized protein (PIWI) monomer, 56 kDa Rhodopseudomonas palustris (strain … protein
Buffer: 20 mM Tris-HCl, pH8.0, 200 mM NaCl, 5 mM MgCl2, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 27
Complex of Rhodopseudomonas palustris pAgo with TIR-like effector protein
Elena Manakova
RgGuinier 3.6 nm
Dmax 12.0 nm
VolumePorod 192 nm3

SASDJ75 – apo Archaeoglobus fulgidus Argonaute protein

Piwi protein AF_1318 experimental SAS data
OTHER model
Sample: Piwi protein AF_1318 dimer, 98 kDa Archaeoglobus fulgidus protein
Buffer: 20 mM TrisHCl, pH 7.5, 5 mM MgCl2, 500 mM NaCl and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Sep 1
Apo Archaeoglobus fulgidus Argonaute protein dimerises in solution
Elena Manakova
RgGuinier 3.8 nm
Dmax 12.1 nm
VolumePorod 174 nm3

SASDH39 – Complex of Archaeoglobus fulgidus Argonaute with dsDNA (5'p-ATTGTACGTACAAT)

Piwi protein AF_13185'-phosphorilated 14-mer DNA oligoduplex experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Piwi protein AF_1318 dimer, 102 kDa Archaeoglobus fulgidus protein
5'-phosphorilated 14-mer DNA oligoduplex dimer, 9 kDa DNA
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 2019 Jul 6
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 11(1):4518 (2021)
...Manakova E, Jankunec M, Silanskas A, Sasnauskas G, Zaremba M
RgGuinier 3.2 nm
Dmax 10.1 nm
VolumePorod 158 nm3

SASDH49 – Complex of Archaeoglobus fulgidus Argonaute monomeric mutant with dsDNA (5'p-ATTGTACGTACAAT)

Piwi protein AF_1318 delta (296-303) mutant5'-phosphorilated 14-mer DNA oligoduplex experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Piwi protein AF_1318 delta (296-303) mutant monomer, 50 kDa Archaeoglobus fulgidus protein
5'-phosphorilated 14-mer DNA oligoduplex dimer, 9 kDa DNA
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 2019 Jul 6
Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 11(1):4518 (2021)
...Manakova E, Jankunec M, Silanskas A, Sasnauskas G, Zaremba M
RgGuinier 2.8 nm
Dmax 9.6 nm
VolumePorod 109 nm3

SASDRX8 – Heterodimeric complex of AfAgo protein Af1318 and AfAgo-N protein (containing N-L1-L2 domains) with a 14 base pair DNA oligoduplex in low salt buffer

Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein)Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains)5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
CUSTOM IN-HOUSE model
Sample: Piwi protein AF_1318 (Archaeoglobus fulgidus AfAgo protein) monomer, 51 kDa Archaeoglobus fulgidus (strain … protein
Uncharacterized protein (AfAgo-N protein containing N-L1-L2 domains) monomer, 31 kDa Archaeoglobus fulgidus DSM … protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH 7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 2.9 nm
Dmax 9.7 nm
VolumePorod 145 nm3

SASDR29 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant in high salt buffer

single-chain full Archaeoglobus fulgidus Argonaute variant experimental SAS data
OTHER model
Sample: single-chain full Archaeoglobus fulgidus Argonaute variant monomer, 78 kDa Archaeoglobus fulgidus protein
Buffer: 20 mM TrisHCl pH 7.5, 500 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Aug 31
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 3.1 nm
Dmax 9.7 nm
VolumePorod 142 nm3

SASDRZ8 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant complexed with an 11 base pair DNA oligoduplex in low salt buffer

single-chain full Archaeoglobus fulgidus Argonaute5'-end phosphorylated DNA guide strand, 11 nt (MZ864)DNA target strand, 11 nt (MZ865) experimental SAS data
CUSTOM IN-HOUSE model
Sample: single-chain full Archaeoglobus fulgidus Argonaute monomer, 78 kDa Archaeoglobus fulgidus protein
5'-end phosphorylated DNA guide strand, 11 nt (MZ864) monomer, 3 kDa DNA
DNA target strand, 11 nt (MZ865) monomer, 3 kDa DNA
Buffer: 20 mM TrisHCl pH7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Aug 31
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 2.9 nm
Dmax 9.6 nm
VolumePorod 125 nm3

SASDRY8 – Single-chain Archaeoglobus fulgidus argonaute fAfAgo-fusion variant complexed with a 14 base pair DNA oligoduplex in low salt buffer

single-chain full Archaeoglobus fulgidus Argonaute5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) experimental SAS data
GASBOR model
Sample: single-chain full Archaeoglobus fulgidus Argonaute monomer, 78 kDa Archaeoglobus fulgidus protein
5'-end phosphorylated DNA oligoduplex, 14 bp (MZ1288) monomer, 9 kDa DNA
Buffer: 20 mM TrisHCl pH7.5, 200 mM NaCl, 5 mM MgCl2, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Jul 6
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res (2024)
Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M
RgGuinier 3.0 nm
Dmax 10.3 nm
VolumePorod 131 nm3