1XR5

Crystal Structure of the RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 14

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual-Function Target for Common Cold Antiviral Therapy

Love, R.A., Maegley, K.A., Yu, X., Ferre, R.A., Lingardo, L.K., Diehl, W., Parge, H.E., Dragovich, P.S., Fuhrman, S.A.

(2004) Structure 12: 1533-1544

  • DOI: 10.1016/j.str.2004.05.024
  • Primary Citation of Related Structures:  
    1XR7, 1XR6, 1XR5

  • PubMed Abstract: 

    • Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets ...

    Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3Dpol, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3Dpol have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3Dpol enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3Dpol provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3Dpol also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

    Organizational Affiliation: 

    Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. robert.love@pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyprotein A466Rhinovirus B14Mutation(s): 0 
Gene Names: P3D
EC: 2.7.7.48 (PDB Primary Data), 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM
Download Ideal Coordinates CCD File 
A
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.326α = 90
b = 97.326β = 90
c = 153.113γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance