3OL7

Poliovirus polymerase elongation complex with CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.226 

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.USA 107: 22505-22510

  • DOI: 10.1073/pnas.1007626107
  • Primary Citation of Related Structures:  

  • 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 developmen ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase
A, E, I, M
471Poliovirus type 1 (strain Mahoney)Mutation(s): 1 
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Go to UniProtKB:  P03300
Entity ID: 2
MoleculeChainsLengthOrganism
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
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*AP*C)-3')C,G,K,O15N/A
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')D,H,L,P9N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

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Download CCD File 
A, E, K, M
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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A, E, I, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
E, I, J, M, N
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, E, I, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A, E, I, M, N, O
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, E, J, N
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.226 
  • 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
d*TREKdata scaling
Blu-Icedata collection
d*TREKdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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