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28 hits found for Becker

SASDF52 – dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE

Dosage compensation regulator experimental SAS data
dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE Rg histogram
Sample: Dosage compensation regulator monomer, 29 kDa Drosophila melanogaster protein
Buffer: 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 29
Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Nucleic Acids Res 47(8):4319-4333 (2019)
...Becker PB, Hennig J
RgGuinier 3.2 nm
Dmax 12.5 nm
VolumePorod 22 nm3

SASDF62 – Mixture of the dsRBD1 and dsRBD2 domains of Drosophila helicase dosage compensation regulator, MLE, and the roX2 RNA stem-loop 7 18mer-fragment, at 1.0 mg/ml

Dosage compensation regulatorroX2 stem-loop 7, 18-mer fragment experimental SAS data
Dosage compensation regulator roX2 stem-loop 7, 18-mer fragment Kratky plot
Sample: Dosage compensation regulator monomer, 29 kDa Drosophila melanogaster protein
roX2 stem-loop 7, 18-mer fragment monomer, 12 kDa synthetic construct RNA
Buffer: 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 29
Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Nucleic Acids Res 47(8):4319-4333 (2019)
...Becker PB, Hennig J
RgGuinier 3.1 nm
Dmax 13.3 nm
VolumePorod 25 nm3

SASDF72 – roX2 RNA stem-loop 7 18mer-fragment

roX2 stem-loop 7, 18-mer fragment experimental SAS data
DAMMIN model
Sample: roX2 stem-loop 7, 18-mer fragment monomer, 12 kDa synthetic construct RNA
Buffer: 20 mM NaPO4, 200 mM NaCl, 1 mM DTT, pH: 6.5
Experiment: SAXS data collected at BM29, ESRF on 2016 Nov 29
Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless. Nucleic Acids Res 47(8):4319-4333 (2019)
...Becker PB, Hennig J
RgGuinier 1.8 nm
Dmax 8.5 nm
VolumePorod 14 nm3

SASDDL2 – Sinorhizobium meliloti Proline Utilization A (PutA) lowest concentration, 1.00 mg/ml

Sinorhizobium meliloti (SmPutA) experimental SAS data
MES-FOXS model
Sample: Sinorhizobium meliloti (SmPutA) monomer, 132 kDa Sinorhizobium meliloti protein
Buffer: 50 mM Tris, 1% (v/v) glycerol, 0.5 mM THP, and 50 mM NaCl, pH: 7.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Mar 27
Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function. J Biol Chem 291(46):24065-24075 (2016)
...Becker DF, Tanner JJ
RgGuinier 3.4 nm
Dmax 11.0 nm
VolumePorod 171 nm3

SASDWL2 – C-terminal mini-Collagen VI heterotrimer

Collagen alpha-1(VI) chainCollagen alpha-2(VI) chain (R680H, K966N, Q967E)Collagen alpha-3(VI) chain (D2357R, K2367R, D2431V, R2441T, R2609A, R2610A) experimental SAS data
ALPHAFOLD model
Sample: Collagen alpha-1(VI) chain , 52 kDa Homo sapiens protein
Collagen alpha-2(VI) chain (R680H, K966N, Q967E) , 53 kDa Homo sapiens protein
Collagen alpha-3(VI) chain (D2357R, K2367R, D2431V, R2441T, R2609A, R2610A) , 54 kDa Homo sapiens protein
Buffer: Tris-buffered saline, pH: 7.4
Experiment: SAXS data collected at B21, Diamond Light Source on 2022 Jul 27
Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations. Nat Commun 16(1):7549 (2025)
...Becker MH, Dajani R, Snee M, Roseman AM, Baldock C
RgGuinier 4.8 nm
Dmax 18.7 nm
VolumePorod 478 nm3

SASDDM2 – Sinorhizobium meliloti Proline Utilization A (PutA) at 2.00 mg/ml

Sinorhizobium meliloti (SmPutA) experimental SAS data
MES-FOXS model
Sample: Sinorhizobium meliloti (SmPutA) monomer, 132 kDa Sinorhizobium meliloti protein
Buffer: 50 mM Tris, 1% (v/v) glycerol, 0.5 mM THP, and 50 mM NaCl, pH: 7.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Mar 27
Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function. J Biol Chem 291(46):24065-24075 (2016)
...Becker DF, Tanner JJ
RgGuinier 3.8 nm
Dmax 11.9 nm
VolumePorod 225 nm3

SASDDN2 – Sinorhizobium meliloti Proline Utilization A (PutA) at 3.00 mg/ml

Sinorhizobium meliloti (SmPutA) experimental SAS data
MES-FOXS model
Sample: Sinorhizobium meliloti (SmPutA) monomer, 132 kDa Sinorhizobium meliloti protein
Buffer: 50 mM Tris, 1% (v/v) glycerol, 0.5 mM THP, and 50 mM NaCl, pH: 7.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Mar 27
Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function. J Biol Chem 291(46):24065-24075 (2016)
...Becker DF, Tanner JJ
RgGuinier 3.8 nm
Dmax 11.8 nm
VolumePorod 248 nm3

SASDDP2 – Sinorhizobium meliloti Proline Utilization A (PutA) at high concentration, 4.00 mg/ml

Sinorhizobium meliloti (SmPutA) experimental SAS data
MES-FOXS model
Sample: Sinorhizobium meliloti (SmPutA) monomer, 132 kDa Sinorhizobium meliloti protein
Buffer: 50 mM Tris, 1% (v/v) glycerol, 0.5 mM THP, and 50 mM NaCl, pH: 7.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2014 Mar 27
Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function. J Biol Chem 291(46):24065-24075 (2016)
...Becker DF, Tanner JJ
RgGuinier 3.9 nm
Dmax 11.9 nm
VolumePorod 277 nm3

SASDDP3 – N-propargyl glycine-Inactivated Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS

Bifunctional protein PutA experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Bifunctional protein PutA dimer, 215 kDa Bradyrhizobium diazoefficiens protein
Buffer: 50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol, pH: 7.8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Jul 16
Redox Modulation of Oligomeric State in Proline Utilization A. Biophys J 114(12):2833-2843 (2018)
...Becker DF, Tanner JJ
RgGuinier 4.6 nm
Dmax 14.4 nm
VolumePorod 324 nm3

SASDDQ3 – Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS

Bifunctional protein PutA experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Bifunctional protein PutA tetramer, 430 kDa Bradyrhizobium diazoefficiens protein
Buffer: 50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol, pH: 7.8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Jul 16
Redox Modulation of Oligomeric State in Proline Utilization A. Biophys J 114(12):2833-2843 (2018)
...Becker DF, Tanner JJ
RgGuinier 5.2 nm
Dmax 14.2 nm
VolumePorod 582 nm3

SASDBV3 – ...Becker muscular dystrophy variant)

Dystrophin central domain repeats 16 to 21 (Δ2146-2305; Becker muscular dystrophy variant, deletion of exons 45-47) experimental SAS data
GASBOR model
Sample: ...Becker muscular dystrophy variant, deletion of exons 45-47) monomer, 64 kDa Homo sapiens protein
Buffer: 20 mM Tris 150 mM NaCl 1 mM EDTA 2% glycerol 5% acetonitrile, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2014 Feb 5
Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions. J Biol Chem 293(18):6637-6646 (2018)
Delalande O, Molza AE, Dos Santos Morais R, Chéron A, Pollet É, Raguenes-Nicol C, Tascon C, Giudice E, Guilbaud M, Nicolas A, Bondon A, Leturcq F, Férey N, Baaden M, Perez J, Roblin P, Piétri-Rouxel F...
RgGuinier 6.0 nm
Dmax 21.0 nm
VolumePorod 184 nm3

SASDNW5 – apo Roquin-1 (coreROQ) at 50 µM, including concentration series data at 100, 200, 300 µM

Roquin-1 experimental SAS data
Roquin-1 Kratky plot
Sample: Roquin-1 monomer, 18 kDa Mus musculus protein
Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.9 nm
Dmax 7.0 nm
VolumePorod 35 nm3

SASDNX5 – apo Roquin-1 (extROQ) at 50 µM, including concentration series data at 100, 200, 300 µM

Roquin-1 extROQ experimental SAS data
Roquin-1 extROQ Kratky plot
Sample: Roquin-1 extROQ monomer, 35 kDa Mus musculus protein
Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 2.8 nm
Dmax 14.0 nm
VolumePorod 53 nm3

SASDNY5 – apo Roquin-1 (Nterm ROQ) at 50 µM, including concentration series data at 100, 300 µM

Roquin-1 Nterm experimental SAS data
Roquin-1 Nterm Kratky plot
Sample: Roquin-1 Nterm monomer, 51 kDa Mus musculus protein
Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.4 nm
Dmax 15.0 nm
VolumePorod 88 nm3

SASDNZ5 – apo Roquin-1 (Nterm A-site mut ROQ) at 50 µM, including concentration series data at 100, 300 µM

Roquin-1 Nterm Amut (K220A, K239A, R260A) experimental SAS data
Roquin-1 Nterm Amut (K220A, K239A, R260A) Kratky plot
Sample: Roquin-1 Nterm Amut (K220A, K239A, R260A) monomer, 51 kDa Mus musculus protein
Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.3 nm
Dmax 14.0 nm
VolumePorod 80 nm3

SASDN26 – apo Roquin-1 (Nterm B-site mut ROQ) at 50 µM, including concentration series data at 100, 300 µM

Roquin-1 Nterm Bmut (R135E, K136E, D322A, K323A) experimental SAS data
Roquin-1 Nterm Bmut (R135E, K136E, D322A, K323A) Kratky plot
Sample: Roquin-1 Nterm Bmut (R135E, K136E, D322A, K323A) monomer, 51 kDa Mus musculus protein
Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.5 nm
Dmax 15.0 nm
VolumePorod 92 nm3

SASDN36 – Ox40 RNA (untranslated region, UTR) full-length

Ox40 3'UTR full-length experimental SAS data
Ox40 3'UTR full-length Kratky plot
Sample: Ox40 3'UTR full-length monomer, 50 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.7 nm
Dmax 12.0 nm
VolumePorod 115 nm3

SASDN46 – Ox40 RNA (untranslated region, UTR) alternative decay element (ADE)

Ox40 3 UTR ADE experimental SAS data
Ox40 3 UTR ADE Kratky plot
Sample: Ox40 3 UTR ADE monomer, 16 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 2.1 nm
Dmax 7.2 nm
VolumePorod 21 nm3

SASDN56 – Ox40 RNA (untranslated region, UTR) constitutive decay element (CDE)

Ox40 3 UTR CDE experimental SAS data
Ox40 3 UTR CDE Kratky plot
Sample: Ox40 3 UTR CDE monomer, 9 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 2.0 nm
Dmax 9.5 nm
VolumePorod 16 nm3

SASDN66 – Ox40 RNA (untranslated region, UTR) alternative and constitutive decay element (ADE-CDE)

Ox40 3 UTR ADE-CDE experimental SAS data
Ox40 3 UTR ADE-CDE Kratky plot
Sample: Ox40 3 UTR ADE-CDE monomer, 24 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 2.6 nm
Dmax 10.0 nm
VolumePorod 26 nm3

SASDN76 – Ox40 RNA (untranslated region, UTR) Bulge

Ox40 3 UTR Bulge experimental SAS data
Ox40 3 UTR Bulge Kratky plot
Sample: Ox40 3 UTR Bulge monomer, 11 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.8 nm
Dmax 6.5 nm
VolumePorod 17 nm3

SASDN86 – Ox40 RNA (untranslated region, UTR) Bulge with alternative decay element (Bulge-ADE)

Ox40 3 UTR Bulge-ADE experimental SAS data
Ox40 3 UTR Bulge-ADE Kratky plot
Sample: Ox40 3 UTR Bulge-ADE monomer, 27 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.3 nm
Dmax 12.5 nm
VolumePorod 37 nm3

SASDE96 – Aldehyde dehydrogenase 12 from Zea mays Extrapolated to Infinite Dilution

Aldehyde dehydrogenase 12 experimental SAS data
ALLOSMOD model
Sample: Aldehyde dehydrogenase 12 tetramer, 242 kDa Zea mays protein
Buffer: 50 mM Tris-HCl, 50 mM NaCl, 0.5 mM TCEP, and 5% (v/v) glycerol, pH: 7.8
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 6
Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants. J Mol Biol (2018)
...Becker DF, Šebela M, Tanner JJ, Kopečný D
RgGuinier 4.1 nm
Dmax 14.4 nm
VolumePorod 351 nm3

SASDN96 – Ox40 RNA (untranslated region, UTR) Bulge with alternative and constitutive decay elements (Bulge-ADE-CDE)

Ox40 3 UTR Bulge-ADE-CDE experimental SAS data
Ox40 3 UTR Bulge-ADE-CDE Kratky plot
Sample: Ox40 3 UTR Bulge-ADE-CDE monomer, 35 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 3.4 nm
Dmax 11.0 nm
VolumePorod 46 nm3

SASDNA6 – Ox40 RNA (untranslated region, UTR) constitutive decay element (CDEshort)

Ox40 3 UTR CDEshort experimental SAS data
Ox40 3 UTR CDEshort Kratky plot
Sample: Ox40 3 UTR CDEshort monomer, 5 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.5 nm

SASDNB6 – Ox40 RNA (untranslated region, UTR) terminal stem (Terminusuucg)

Ox40 3 UTR Terminusuucg experimental SAS data
Ox40 3 UTR Terminusuucg Kratky plot
Sample: Ox40 3 UTR Terminusuucg monomer, 10 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.6 nm
Dmax 5.5 nm
VolumePorod 16 nm3

SASDNC6 – Ox40 RNA (untranslated region, UTR), alternative decay element (ADEshort)

Ox40 3 UTR ADEshort experimental SAS data
Ox40 3 UTR ADEshort Kratky plot
Sample: Ox40 3 UTR ADEshort monomer, 7 kDa Mus musculus RNA
Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res (2022)
...Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
RgGuinier 1.7 nm
Dmax 9.0 nm
VolumePorod 12 nm3

SASDB27 – Chimeric EcRHH-RcPutA: The E.coli Proline utilization A RHH domain fused to R.capsulatus PutA

Proline utilization A experimental SAS data
Proline utilization A Kratky plot
Sample: Proline utilization A dimer, 251 kDa Escherchia coli, Rhodobacter … protein
Buffer: 50 mM Tris, 200 mM NaCl, 0.5 mM Tris(3-hydroxypropyl)phosphine, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2012 Oct 16
Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA. Biosci Rep 36(6) (2016)
...Becker DF
RgGuinier 5.2 nm
Dmax 18.3 nm
VolumePorod 308 nm3