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 1.4 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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase
A, E, I, M
471Poliovirus 1Mutation(s): 1 
Gene Names: 3D
EC: 2.7.7.48
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
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
26N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*AP*C)-3')
C, G, K, O
15N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3')
D, H, L, P
9N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / 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
PEG
Query on PEG

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CB [auth N],
GA [auth E],
RA [auth J],
X [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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DB [auth N]
HA [auth E]
MA [auth I]
NA [auth I]
OA [auth I]
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
ZN
Query on ZN

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AB [auth M],
IA [auth E],
QA [auth I],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA
Query on IPA

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BB [auth N]
CA [auth E]
DA [auth E]
EA [auth E]
EB [auth O]
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
MG
Query on MG

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AA [auth E]
JA [auth I]
Q [auth A]
R [auth A]
UA [auth M]
AA [auth E],
JA [auth I],
Q [auth A],
R [auth A],
UA [auth M],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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

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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
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description