2ARI
Solution structure of micelle-bound fusion domain of HIV-1 gp41
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_HNCO; 3D_HNCA; 3D_HN(CO)CA; 3D_HN(CA)CB; 2D_HNCG | 0.7 mM HIV-1 gp41 fusion domain U-2H, 13C, 15N; 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O | 93% H2O/7% D2O | 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate; 0.05% (w/v) sodium azide | 6.5 | ambient | 298 | |
| 2 | 3D_15N-separated_TOCSY; 3D_15N-separated_NOESY; 3D_HNHA | 0.7 mM HIV-1 gp41 fusion domain U-15N; 75 mM sodium dodecyl sulfate deuterated; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O | 93% H2O/7% D2O | 75 mM sodium dodecyl sulfate deuterated; 25 mM sodium phosphate; 0.05% (w/v) sodium azide | 6.5 | ambient | 298 | |
| 3 | 2D_IPAP-HSQC_JNH; 3D_HNCO_JNH; 3D_QJ-HNCO_JNCO; 3D_HNCO_JCOCA; 3D_HN(CO)CA_JCACB | 0.7 mM HIV-1 gp41 fusion domain U-2H, 13C, 15N; 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate buffer pH 6.5; 0.05% (w/v) sodium azide; 93% H2O, 7% D2O; sample aligned with respect to the magnetic field using a stretched polyacryalmide gel | 93% H2O/7% D2O | 75 mM sodium dodecyl sulfate; 25 mM sodium phosphate; 0.05% (w/v) sodium azide | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 600 |
| 2 | Bruker | DRX | 600 |
| 3 | Bruker | DMX | 750 |
| 4 | Bruker | DRX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing molecular dynamics | The structures are based on a total of 192 restraints. 57 are residual dipolar coupling (RDC) restraints, 74 are NOE-derived distance restraints, 38 are TALOS-derived loose (minimum +/- 30 degrees from target value) dihedral angle restraints, and 23 are 3J_HNHA restraints. Note that RDC restraints were included only for the least mobile residues Ile-4 to Met-19 (with S2 > 0.65), dihedral restraints were included for residues Ile-4 to Ala-22, NOE and 3J_HNHA restraints were included for residues Val-2 to Met-24. Also note that the residue index in PDB and constraints files is such that HIV-1 gp41 fusion domain residue i is actually labeled as i+1. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 30 |
| Conformers Submitted Total Number | 30 |
| Representative Model | 1 (best agreement with measured residual dipolar couplings) |
| Additional NMR Experimental Information | |
|---|---|
| Details | The structure was determined using triple-resonance NMR spectroscopy. Residual dipolar couplings were measured for a peptide-micelle complex aligned with respect to the magnetic field using a stretched polyacryamide gel. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker |
| 2 | collection | XwinNMR | 3.5 | Bruker |
| 3 | processing | NMRPipe | 2.3 | Delaglio |
| 4 | data analysis | NMRPipe | 2.3 | Delaglio |
| 5 | data analysis | Sparky | 3.11 | Goddard |
| 6 | refinement | X-PLOR-NIH | 2.9.4 | Schwieters |
