Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for differential binding of hnRNP Splicing Auxiliary Factors
SOLUTION NMR - SOLUTION SCATTERING
Solution Scattering Data Acquistion | 1 |
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Scattering Type | neutron |
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Radiation/Neutron Source | APS BioCat 18ID beam line |
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Synchrotron | Y |
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Beamline Type | APS |
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Detector Type | |
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Detector Manufacturer Details | |
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Temperature (K) | 298 |
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pH | 6.2 |
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Numer of Time Frames Used | |
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Protein Concentration Range (mg/mL) | 6-6.5 |
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Sample Buffer | 20 mM Bis-Tris, 20 mM NaCl, pH 6.2 |
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Data Reduction Software | GNOM |
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Guiner Mean Radius Of Gyration (nm) | 2.1 |
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Sigma Mean Radius Of Gyration | 0.1 |
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R(XS-1) Mean Cross Sectional Radii (nm) | |
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R(XS-1) Sigma Mean Cross Sectional Radii | |
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R(XS-2) Mean Cross Sectional Radii (nm) | |
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R(XS-2) Sigma Mean Cross Sectional Radii | |
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P(R) Protein Length (nm) | 6.9 |
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Solution Scattering Data Analysis and Model Fitting |
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Method | Software | Software Authors | Starting Model | Conformers, Number Calculated | Conformers, Number Submitted | Conformers, Selection Criteria | Best Representative Conformer | Other Details |
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NMR, SAXS | NMRpipe, NMRViewJ ,X-PLOR_NIH, AMBER, GNOM | Frank Delaglio; Ad Bax; Bruce Johnson; Charles Schwieters; Marius Clore; David Case; Dmitry Svergun | | 1024 | 10 | Lowest energy | 10 | |
NMR Experiment |
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
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1 | 2D 1H-1H NOESY | 400 uM ESS2p | 90% H2O/10% D2O | 5 mM | 6.5 | 1 atm | 283 | Bruker AVANCE NEO 700 |
2 | 2D 1H-13C HMQC | 400 uM [U-100% 13C; U-100% 15N on ATP and GTP ESS2p | 100% D2O | 5 mM | 6.5 | 1 atm | 298 | Bruker AVANCE II 900 |
3 | 2D 1H-1H NOESY | 450 uM selective deuteration ESS2p | 100% D2O | 5 mM | 6.5 | 1 atm | 298 | Bruker AVANCE II 800 |
4 | 2D 1H-1H TOCSY | 400 uM ESS2p | 90% H2O/10% D2O | 5 mM | 6.5 | 1 atm | 298 | Bruker AVANCE II 800 |
5 | 2D 1H-15N HSQC | 300 uM Uniform_15N on GTP and UTP ESS2p | 90% H2O/10% D2O | 5 mM | 6.5 | 1 atm | 283 | Bruker AVANCE II 800 |
6 | 2D 1H-15N HNN-COSY | 300 uM Uniform_15N on all nucleotides ESS2p | 90% H2O/10% D2O | 5 mM | 6.5 | 1 atm | 283 | Bruker AVANCE II 900 |
NMR Spectrometer Information |
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Spectrometer | Manufacturer | Model | Field Strength |
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1 | Bruker | AVANCE II | 900 |
2 | Bruker | AVANCE II | 800 |
3 | Bruker | AVANCE NEO | 700 |
NMR Refinement |
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Method | Details | Software |
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molecular dynamics | | Amber |
NMR Ensemble Information |
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Conformer Selection Criteria | structures with the lowest energy |
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Conformers Calculated Total Number | 1024 |
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Conformers Submitted Total Number | 10 |
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Representative Model | 1 (lowest energy) |
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Computation: NMR Software |
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# | Classification | Version | Software Name | Author |
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1 | refinement | Amber | | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman |
2 | structure calculation | X-PLOR NIH | | Schwieters, Kuszewski, Tjandra and Clore |
3 | chemical shift assignment | NMRViewJ | | Bruce Johnson |
4 | collection | TopSpin | | Bruker Biospin |
5 | processing | NMRPipe | | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
6 | data analysis | NMRFAM-SPARKY | | Woonghee Lee, Marco Tonelli, John L Markley |