Experiment: 7RNO

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