2D19
Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the kissing-loop dimer
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O | 50mM NaCl | 7.0 | ambient | 283 | |
2 | 1D-HSQC-selected spectrum | 0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O | 50mM NaCl | 7.0 | ambient | 283 | |
3 | 1D-HSQC-filtered spectrum | 0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O | 50mM NaCl | 7.0 | ambient | 283 | |
4 | 2D NOESY | 1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O | 50mM NaCl | 7.0 | ambient | 283 | |
5 | 2D TOCSY | 1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 | |
6 | 2D NOESY | 1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 | |
7 | 2D-w2-filtered NOESY | 0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 | |
8 | 2D-w2-filtered NOESY | 0.1mM [A-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 | |
9 | 2D TOCSY | 1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 | |
10 | 2D NOESY | 1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O | 100% D2O | 50mM NaCl | 7.0 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structures are based on a total of 502 restraints, 286 are NOE-derived distance constraints, 140 dihedral angle restraints, 76 distance restraints from hydrogen bonds. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 11 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | Chemical synthesized 25-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [A-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized 39-mer RNA corresponding to the HIV-1 dimerization initiation site. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | XwinNMR | 2.6 | BRUKER |
2 | data analysis | Felix | 97.0 | Molecular Simulations |
3 | structure solution | Discover | 97.0 | Accelrys |
4 | refinement | Discover | 97.0 | Accelrys |