Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.79 kDa 
• Atom Count: 2147 
• Modelled Residue Count: 257 
• Deposited Residue Count: 393 
• Unique protein chains: 1

1RAJ

Poliovirus Polymerase with a 68 residue N-terminal truncation

• PDB DOI: 10.2210/pdb1RAJ/pdb

• Classification: TRANSFERASE
• Organism(s): Human poliovirus 1 Mahoney
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-10-31 Released: 2004-08-17 
• Deposition Author(s): Thompson, A.A., Peersen, O.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.242 

Literature

Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase.

Thompson, A.A., Peersen, O.B.

(2004) EMBO J 23: 3462-3471

• PubMed: 15306852 
• DOI: 10.1038/sj.emboj.7600357
• Primary Citation of Related Structures:  
  1RA6, 1RA7, 1RAJ, 1TQL


• PubMed Abstract: 
  

The active RNA-dependent RNA polymerase of poliovirus, 3Dpol, is generated by cleavage of the 3CDpro precursor protein, a protease that has no polymerase activity despite containing the entire polymerase domain. By intentionally disrupting a known and persistent crystal packing interaction, we have crystallized the poliovirus polymerase in a new space group and solved the complete structure of the protein at 2.0 A resolution. It shows that the N-terminus of fully processed 3Dpol is buried in a surface pocket where it makes hydrogen bonds that act to position Asp238 in the active site. Asp238 is an essential residue that selects for the 2' OH group of substrate rNTPs, as shown by a 2.35 A structure of a 3Dpol-GTP complex. Mutational, biochemical, and structural data further demonstrate that 3Dpol activity is exquisitely sensitive to mutations at the N-terminus. This sensitivity is the result of allosteric effects where the structure around the buried N-terminus directly affects the positioning of Asp238 in the active site.

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Organizational Affiliation: 

Program in Cellular and Molecular Biology, Colorado State University, Fort Collins 80523, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	393	Human poliovirus 1 Mahoney	Mutation(s): 2  Gene Names: 3D EC: 2.7.7.48 (PDB Primary Data), 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt)
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.242 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.71	α = 90
b = 87.71	β = 90
c = 107.34	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-31 
• Released Date: 2004-08-17 
Deposition Author(s): Thompson, A.A., Peersen, O.B.

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references