1QA5
MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 1H | 4.6 | 285 | |||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AMX | 500 |
| 2 | Bruker | DMX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| DISTANCE GEOMETRY, SIMULATED ANNEALING | THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYR-2-57) SOLVED BY TWO-DIMENSIONAL HOMONUCLEAR NMR SPECTROSCOPY IS BASED ON 540 EXPERIMENTAL RESTRAINTS: 332 INTRARESIDUAL, 156 SEQUENTIAL AND MEDIUM RANGE (1<=|I-J|<=4), AND 10 LONG RANGE (|I-J|>=5) INTERPROTON DISTANCE RESTRAINTS; 42 TORSION ANGLE RESTRAINTS (PHI). NO RESTRAINTS FOR HYDROGEN BONDS WERE ADDED. | X-PLOR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN |
| Conformers Calculated Total Number | 400 |
| Conformers Submitted Total Number | 2 |
| Representative Model | 1 (n/a) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE STRUCTURE OF THE MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT WELL DEFINED BY NMR RESTRAINTS. ONLY TWO SECONDARY STRUCTURE ELEMENTS CAN BE OBSERVED: A FIRST HELIX IN THE POSITIVE CLUSTER REGION FROM PRO14 TO ARG22 AND A SECOND HELICAL REGION FROM ALA33 TO GLY41. ADDITIONALLY, THE N-TERMINAL MYRISTIC ACID RESIDUE CLOSELY INTERACTS WITH THE SIDE CHAIN OF TRP5 AND THEREBY FORMS A LOOP WITH GLY2, GLY3 AND LYS4 IN THE KINK REGION. TWO MODELS ARE PRESENTED TO DEMONSTRATE THE CONFORMATIONAL VARIETY OF THE STRUCTURES CALCULATED. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR | 3.851 | BRUNGER |
| 2 | structure calculation | AURELIA | 2.0 | Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzer |
| 3 | structure calculation | X-PLOR | 3.851 | BRUNGER |
