Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated docking, NMR and restrained MD
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-13C HMQC | 100 uM hpMR1 (human platform MR1), 100 uM [U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2] bovine beta 2 microglobulin, 300 uM TAPBPR | 90% H2O/10% D2O | 50 mM | 7.2 | 1.01325 bar | 298.15 | Bruker AVANCE III 600 |
| 2 | 2D 1H-13C HMQC | 100 uM hpMR1 (human platform MR1), 100 uM [U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2] bovine beta 2 microglobulin, 300 uM TAPBPR | 90% H2O/10% D2O | 50 mM | 7.2 | 1.01325 bar | 298.15 | Bruker AVANCE III 600 |
| 3 | 3D NOESY HMQC | 100 uM hpMR1 (human platform MR1), 100 uM [U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2] bovine beta 2 microglobulin, 300 uM TAPBPR | 90% H2O/10% D2O | 50 mM | 7.2 | 1.01325 bar | 298.15 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 600 |
| 2 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | HADDOCK in combination with NMR derived chemical shift perturbations was used to generate the initial model of the complex. The TAP binding protein-like variant starting structure is PDB ID 5WER chain C. The major histocompatibility complex class I-related gene protein and beta-2-microglobulin are homology modeled based on PDB ID 4PJ5 chain A and chain B. | GROMACS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 10000 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | GROMACS | v2020.4 | Department of Biophysical Chemistry, University of Groningen, Netherlands |
| 2 | structure calculation | HADDOCK | Bonvin | |
| 3 | chemical shift assignment | NMRFAM-SPARKY | Woonghee Lee, Marco Tonelli, and John L. Markley | |
| 4 | peak picking | NMRFAM-SPARKY | Woonghee Lee, Marco Tonelli, and John L. Markley | |
