6BG9

HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL

Summary for 6BG9

• Entry DOI: 10.2210/pdb6bg9/pdb
• EMDB information: 7080
• NMR Information: BMRB: 27289
• Descriptor: RNA dimerization signal (1 entity in total)
• Functional Keywords: rna inernal loops, sheared ga pairs, gu wobble, s-turn thermodynamics, rna
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 30718.48

Authors

Summers, M.F. (deposition date: 2017-10-27, release date: 2018-02-21, Last modification date: 2024-05-01)

Primary citation

Zhang, K.,Keane, S.C.,Su, Z.,Irobalieva, R.N.,Chen, M.,Van, V.,Sciandra, C.A.,Marchant, J.,Heng, X.,Schmid, M.F.,Case, D.A.,Ludtke, S.J.,Summers, M.F.,Chiu, W.
Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.
Structure, 26:490-498.e3, 2018

PubMed Abstract: Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.

PubMed: 29398526
DOI: 10.1016/j.str.2018.01.001

Experimental method

ELECTRON MICROSCOPY (9 Å)
SOLUTION NMR (9 Å)