2L1F

Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	400-800 uM [U-2H] RNA (65-MER)	100% D2O	80	7.0	ambient atm	310
2	2D NOESY	400-800 uM [U-2H] RNA (65-MER)	100% D2O	80	7.0	ambient atm	310

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	800
2	Bruker	DRX	600

NMR Refinement
Method	Details	Software
distance geometry	Structures were calculated and refined with CYANA using the AMBER residue library. Upper-limit distance restraints of 2.7 , 3.3 and 5.0 were employed for direct NOE cross peaks of strong, medium and weak intensities, respectively, for all cross peaks except those associated with the intraresidue H8/6-to-H2 and H3 interactions. For these proton pairs, upper distance limits of 4.2 and 3.2 were therefore employed for NOEs of medium and strong intensity, respectively.43 Cross-helix P-P distance restraints (with 20% weighting coefficient) were employed for A-form helical segments to prevent the generation of structures with collapsed major grooves:43,52,55 P(i)-P(i+2) (cross-helix phosphorus of the i+2 base pair) = 16.1 - 17.1 , P(i)-P(i+3) = 14.2 - 15.2 ; P(i)-P(i+4) = 11.7 -12.7 ; P(i)-P(i+5) = 9.4 -10.4 ; P(i)-P(i+6) = 9.0 -10.0 . Torsion angle restraints for A helical stem residues were centered around published A-form RNA values 112 with allowed deviations of 50 degrees. Four restraints per hydrogen bond were employed to enforce approximately linear NH-N and NH-O bond distances of 1.85 0.05, and two lower limit restraints per base pair were employed to weakly enforce base pair planarity (20% weighting coefficient) (G-C base pairs: G-C4 to C-C6 > 8.3 and G-N9 to C-H6 > 10.75 . A-U base pairs: A-C4 to U-C6 > 8.3 and A-N9 to U-H6 > 10.75 ).	CYANA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	340
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
2	refinement	CYANA	2.1	Guntert, Mumenthaler and Wuthrich

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.