2D1B | pdb_00002d1b

Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM NaCl	7.0	ambient	283
2	1D-HSQC-selected spectrum	0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM NaCl	7.0	ambient	283
3	1D-HSQC-filtered spectrum	0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM NaCl	7.0	ambient	283
4	2D NOESY	1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM NaCl	7.0	ambient	283
5	2D TOCSY	1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298
6	2D NOESY	1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298
7	2D-w2-filtered NOESY	0.3mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298
8	2D-w2-filtered NOESY	0.1mM [A-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298
9	2D TOCSY	1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298
10	2D NOESY	1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O	100% D2O	50mM NaCl	7.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500
2	Bruker	DRX	600

NMR Refinement
Method	Details	Software
minimization of model RNA	Solution structures of DIS39 were constructed by combining the structure parts. Structures of the loop region of the kissing-loop dimer (2D19) and stem-bulge-stem region (2D17) were combined by superimposing the two base pairs, C12:G26 and U13:G25.	Discover

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	1
Conformers Submitted Total Number	1
Representative Model	1 (model structure)

Additional NMR Experimental Information
Details	model structure was constructed by combining the structure parts

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Discover	97.0	Accelrys

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.