2L1F

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

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 340 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.2 of the entry. See complete history. 


Literature

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

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.

(2010) J Mol Biol 404: 751-772

  • DOI: 10.1016/j.jmb.2010.09.009
  • Primary Citation of Related Structures:  
    2L1F

  • 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 ...

    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.

    Organizational Affiliation: 

    Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (65-MER)A 65Moloney murine leukemia virus
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (66-MER)B 66Moloney murine leukemia virus
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 340 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2L1F Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Database references, Other