2L1F

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

Summary for 2L1F

• Entry DOI: 10.2210/pdb2l1f/pdb
• NMR Information: BMRB: 17083
• Descriptor: RNA (65-MER), RNA (66-MER) (2 entities in total)
• Functional Keywords: rna, retrovirus, packaging, cryo-et
• Biological source: Moloney Murine Leukemia Virus; More
• Total number of polymer chains: 2
• Total formula weight: 42488.47

Authors

Summers, M.F.,Irobalieva, R.N.,Tolbert, B.,Smalls-Manty, A.,Iyalla, K.,Loeliger, K.,D'Souza, V.,Khant, H.,Schmid, M.,Garcia, E.,Telesnitsky, A.,Chiu, W.,Miyazaki, Y. (deposition date: 2010-07-28, release date: 2010-10-27, Last modification date: 2024-05-01)

Primary citation

Miyazaki, Y.,Irobalieva, R.N.,Tolbert, B.S.,Smalls-Mantey, A.,Iyalla, K.,Loeliger, K.,D'Souza, V.,Khant, H.,Schmid, M.F.,Garcia, E.L.,Telesnitsky, A.,Chiu, W.,Summers, M.F.
Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography.
J.Mol.Biol., 404:751-772, 2010

PubMed Abstract: The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming "kissing" interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney murine leukemia virus ([Ψ(CD)](2), 132 nt, 42.8 kDa) using a (2)H-edited NMR-spectroscopy-based approach. This approach enabled the detection of (1)H-(1)H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional (1)H-(1)H correlated and (1)H-(13)C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D' and SLC' to SL-D) and stack in an end-to-end manner (SL-C to SL-D and SL-C' to SL-D') that gives rise to an elongated overall shape (ca 95 Å×45 Å×25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [Ψ(CD)](2) simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [Ψ(CD)](2) functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins.

PubMed: 20933521
DOI: 10.1016/j.jmb.2010.09.009

Experimental method

SOLUTION NMR