Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 281.20 kDa 
• Atom Count: 18452 
• Modelled Residue Count: 1986 
• Deposited Residue Count: 2082 
• Unique protein chains: 1
• Unique nucleic acid chains: 3
• Unique hybrid chains: 1

3OLA

Poliovirus polymerase elongation complex with 2'-deoxy-CTP

• PDB DOI: 10.2210/pdb3OLA/pdb
• NDB: NA0706

• Classification: TRANSFERASE/RNA
• Organism(s): Human poliovirus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-08-25 Released: 2010-12-22 
• Deposition Author(s): Gong, P., Peersen, O.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

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

• PubMed: 21148772 
• DOI: 10.1073/pnas.1007626107
• Primary Citation of Related Structures:  
  3OL6, 3OL7, 3OL8, 3OL9, 3OLA, 3OLB


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase	A, E, I, M	471	Human poliovirus 1	Mutation(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 B3VQP5 (Human poliovirus 1) Explore B3VQP5  Go to UniProtKB:  B3VQP5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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, N	26	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-D(P*C)-3')	C, G	15	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')	D, H, L, P	9	N/A

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3')	K, O	14	N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	GA [auth K], KA [auth O]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
PEG	EA [auth I], U [auth A], V [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	FA [auth I], W [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	BA [auth I], HA [auth M], Q [auth A], X [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	AA [auth E], CA [auth I], DA [auth I], IA [auth M], JA [auth M], R [auth A], S [auth A], T [auth A], Y [auth E], Z [auth E]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.562	α = 83.57
b = 60.56	β = 83.56
c = 192.832	γ = 77.59

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-25 
• Released Date: 2010-12-22 
Deposition Author(s): Gong, P., Peersen, O.B.

Revision History  

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