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TitleStructure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.
Journal, issue, pagesStructure, Vol. 26, Issue 3, Page 490-498.e3, Year 2018
Publish dateMar 6, 2018
AuthorsKaiming Zhang / Sarah C Keane / Zhaoming Su / Rossitza N Irobalieva / Muyuan Chen / Verna Van / Carly A Sciandra / Jan Marchant / Xiao Heng / Michael F Schmid / David A Case / Steven J Ludtke / Michael F Summers / Wah Chiu /
PubMed AbstractCryoelectron 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, ...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.
External linksStructure / PubMed:29398526 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging) / NMR (solution)
Resolution9.0 - 9.3 Å
Structure data

EMDB-7079:
Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach
Method: EM (single particle) / Resolution: 9.0 Å

7080

6bg9

EMDB-7080: Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach
PDB-6bg9: HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL
Method: EM (single particle) / Resolution: 9.3 Å

Source
  • homo sapiens (human)
KeywordsRNA / RNA INERNAL LOOPS / SHEARED GA PAIRS / GU WOBBLE / S-TURN THERMODYNAMICS

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