4K4W

Poliovirus polymerase elongation complex (r5+2_form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.

Gong, P.Kortus, M.G.Nix, J.C.Davis, R.E.Peersen, O.B.

(2013) Plos One 8: e60272-e60272

  • DOI: 10.1371/journal.pone.0060272
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymer ...

    RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase 3D-POL
A, E
471Poliovirus type 1 (strain Mahoney)Mutation(s): 2 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*GP*GP*AP*GP*AP*UP*GP*AP*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP*GP*AP*AP*A)-3')B,F35N/A
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*C)-3')C,G18N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 64.487α = 73.65
b = 64.367β = 73.56
c = 102.285γ = 72.20
Software Package:
Software NamePurpose
d*TREKdata reduction
PDB_EXTRACTdata extraction
d*TREKdata scaling
Blu-Icedata collection
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references