4A8F

Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation.

Wright, S.Poranen, M.M.Bamford, D.H.Stuart, D.I.Grimes, J.M.

(2012) J Virol 86: 2837

  • DOI: https://doi.org/10.1128/JVI.05168-11
  • Primary Citation of Related Structures:  
    4A8F, 4A8K, 4A8M, 4A8O, 4A8Q, 4A8S, 4A8W, 4A8Y

  • PubMed Abstract: 

    RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage ϕ6 uses the bound noncatalytic Mn(2+) to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn(2+), which must be replaced for elongation to occur. By inserting a dysfunctional Mg(2+) at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASE
A, B, C
665Cystovirus phi6Mutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P11124 (Pseudomonas phage phi6)
Explore P11124 
Go to UniProtKB:  P11124
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11124
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*DAP*GP*CP*GP)-3'D [auth G]4synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
K [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.915α = 90
b = 91.766β = 101.25
c = 140.461γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description