2MQV

Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing.

Miller, S.B.Yildiz, F.Z.Lo, J.A.Wang, B.D'Souza, V.M.

(2014) Nature 515: 591-595

  • DOI: 10.1038/nature13709
  • Primary Citation of Related Structures:  2MQT, 2MS0, 2MS1

  • PubMed Abstract: 
  • To prime reverse transcription, retroviruses require annealing of a transfer RNA molecule to the U5 primer binding site (U5-PBS) region of the viral genome. The residues essential for primer annealing are initially locked in intramolecular interactio ...

    To prime reverse transcription, retroviruses require annealing of a transfer RNA molecule to the U5 primer binding site (U5-PBS) region of the viral genome. The residues essential for primer annealing are initially locked in intramolecular interactions; hence, annealing requires the chaperone activity of the retroviral nucleocapsid (NC) protein to facilitate structural rearrangements. Here we show that, unlike classical chaperones, the Moloney murine leukaemia virus NC uses a unique mechanism for remodelling: it specifically targets multiple structured regions in both the U5-PBS and tRNA(Pro) primer that otherwise sequester residues necessary for annealing. This high-specificity and high-affinity binding by NC consequently liberates these sequestered residues--which are exactly complementary--for intermolecular interactions. Furthermore, NC utilizes a step-wise, entropy-driven mechanism to trigger both residue-specific destabilization and residue-specific release. Our structures of NC bound to U5-PBS and tRNA(Pro) reveal the structure-based mechanism for retroviral primer annealing and provide insights as to how ATP-independent chaperones can target specific RNAs amidst the cellular milieu of non-target RNAs.


    Organizational Affiliation

    1] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Department of Biology, Georgetown University, Washington DC 20057, USA. [3].




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleocapsid protein p10
A
56Moloney murine leukemia virusGene Names: gag-pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (68-MER)B68Murine leukemia virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references