3OL7

Poliovirus polymerase elongation complex with CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.

Gong, P.Peersen, O.B.

(2010) Proc Natl Acad Sci U S A 107: 22505-22510

  • DOI: 10.1073/pnas.1007626107
  • Primary Citation of Related Structures:  
    3OLA, 3OLB, 3OL8, 3OL9, 3OL6, 3OL7

  • PubMed Abstract: 
  • Positive-strand RNA viruses include a large number of human and animal pathogens whose essential RNA-dependent RNA polymerases (RdRPs) share a structurally homologous core with an encircled active site. RdRPs are targets for antiviral drug development, but these efforts are hindered by limited structural information about the RdRP catalytic cycle ...

    Positive-strand RNA viruses include a large number of human and animal pathogens whose essential RNA-dependent RNA polymerases (RdRPs) share a structurally homologous core with an encircled active site. RdRPs are targets for antiviral drug development, but these efforts are hindered by limited structural information about the RdRP catalytic cycle. To further our understanding of RdRP function, we assembled, purified, and then crystallized poliovirus elongation complexes after multiple rounds of nucleotide incorporation. Here we present structures capturing the active polymerase and its nucleotide triphosphate complexes in four distinct states, leading us to propose a six-state catalytic cycle involving residues that are highly conserved among positive-strand RNA virus RdRPs. The structures indicate that RdRPs use a fully prepositioned templating base for nucleotide recognition and close their active sites for catalysis using a novel structural rearrangement in the palm domain. The data also suggest that translocation by RDRPs may not be directly linked to the conformational changes responsible for active site closure and reopening.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PolymeraseA, E, I, M471Human poliovirus 1Mutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*GP*AP*AP*A)-3')B, F, J, N26N/A
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*AP*C)-3')C, G, K, O15N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')D, H, L, P9N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      POP
      Query on POP

      Download Ideal Coordinates CCD File 
      BA [auth E], S [auth A], TA [auth K], VA [auth M]PYROPHOSPHATE 2-
      H2 O7 P2
      XPPKVPWEQAFLFU-UHFFFAOYSA-L
       Ligand Interaction
      PEG
      Query on PEG

      Download Ideal Coordinates CCD File 
      CB [auth N], GA [auth E], RA [auth J], X [auth A]DI(HYDROXYETHYL)ETHER
      C4 H10 O3
      MTHSVFCYNBDYFN-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      DB [auth N], HA [auth E], MA [auth I], NA [auth I], OA [auth I], PA [auth I], SA [auth J], ZA [auth M]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      AB [auth M], IA [auth E], QA [auth I], Y [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      IPA
      Query on IPA

      Download Ideal Coordinates CCD File 
      BB [auth N] , CA [auth E] , DA [auth E] , EA [auth E] , EB [auth O] , FA [auth E] , KA [auth I] , LA [auth I] , 
      BB [auth N],  CA [auth E],  DA [auth E],  EA [auth E],  EB [auth O],  FA [auth E],  KA [auth I],  LA [auth I],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  WA [auth M],  XA [auth M],  YA [auth M]
      ISOPROPYL ALCOHOL
      C3 H8 O
      KFZMGEQAYNKOFK-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      AA [auth E], JA [auth I], Q [auth A], R [auth A], UA [auth M], Z [auth E]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.290 
      • R-Value Work: 0.226 
      • R-Value Observed: 0.229 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 60.724α = 83.01
      b = 60.769β = 82.93
      c = 192.969γ = 77.12
      Software Package:
      Software NamePurpose
      Blu-Icedata collection
      PHASERphasing
      PHENIXrefinement
      d*TREKdata reduction
      d*TREKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-12-22
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2012-09-05
        Changes: Derived calculations
      • Version 1.3: 2017-11-08
        Changes: Refinement description