1WAC

Back-priming mode of Phi6 RNA-dependent RNA polymerase

• PDB DOI: https://doi.org/10.2210/pdb1WAC/pdb

• Classification: POLYMERASE
• Organism(s): Cystovirus phi6
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-26 Released: 2005-01-27 
• Deposition Author(s): Laurila, M.R.L., Salgado, P.S., Stuart, D.I., Grimes, J.M., Bamford, D.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Back-Priming Mode of Phi6 RNA-Dependent RNA Polymerase

Laurila, M.R.L., Salgado, P.S., Stuart, D.I., Grimes, J.M., Bamford, D.H.

(2005) J Gen Virol 86: 521

• PubMed: 15659773 
• DOI: https://doi.org/10.1099/vir.0.80492-0
• Primary Citation of Related Structures:  
  1WAC


• PubMed Abstract: 
  

  The RNA-dependent RNA polymerase of the double-stranded RNA bacteriophage phi6 is capable of primer-independent initiation, as are many RNA polymerases. The structure of this polymerase revealed an initiation platform, composed of a loop in the C-terminal domain (QYKW, aa 629-632), that was essential for de novo initiation. A similar element has been identified in hepatitis C virus RNA-dependent RNA polymerase. Biochemical studies have addressed the role of this platform, revealing that a mutant version can utilize a back-priming initiation mechanism, where the 3' terminus of the template adopts a hairpin-like conformation. Here, the mechanism of back-primed initiation is studied further by biochemical and structural methods.

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Organizational Affiliation: 

Institute of Biotechnology and Department of Biological and Environmental Sciences, Viikki Biocenter, PO Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 223.32 kDa 
• Atom Count: 15,693 
• Modelled Residue Count: 1,986 
• Deposited Residue Count: 1,986 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2 PROTEIN	A, B, C	662	Cystovirus phi6	Mutation(s): 1  EC: 2.7.7.48
UniProt
Find proteins for P11124 (Pseudomonas phage phi6) Explore P11124  Go to UniProtKB:  P11124

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.579	α = 90
b = 105.851	β = 98.86
c = 157.712	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-27 
Deposition Author(s): Laurila, M.R.L., Salgado, P.S., Stuart, D.I., Grimes, J.M., Bamford, D.H.

Revision History  

• Version 1.0: 2005-01-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description