6KWR

Crystal structure of enterovirus 71 polymerase elongation complex (ddCTP form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability.

Shi, W.Ye, H.Q.Deng, C.L.Li, R.Zhang, B.Gong, P.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz1170
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation compl ...

    The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end guanosine of the downstream RNA template interacts with a fingers domain pocket, with the base sandwiched by H44 and R277 side chains through hydrophobic stacking interactions, and these interactions are still maintained after one in-crystal translocation event induced by nucleotide incorporation, implying that the pocket could regulate the functional properties of the polymerase by interacting with RNA. When mutated, residue R277 showed an impact on virus proliferation in virological studies with residue H44 having a synergistic effect. In vitro biochemical data further suggest that mutations at these two sites affect RNA binding, EC stability, but not polymerase catalytic rate (kcat) and apparent NTP affinity (KM,NTP). We propose that, although rarely captured by crystallography, similar surface pocket interaction with nucleobase may commonly exist in nucleic acid motor enzymes to facilitate their processivity. Potential applications in antiviral drug and vaccine development are also discussed.


    Organizational Affiliation

    Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin 300350, China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
A
468Human enterovirus 71Mutation(s): 0 
Find proteins for A0A023RBB6 (Human enterovirus 71)
Go to UniProtKB:  A0A023RBB6
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (31-MER)B31synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))-3')C13synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DCT
Query on DCT

Download SDF File 
Download CCD File 
A
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
C
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.008α = 90.00
b = 76.454β = 94.92
c = 68.075γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-09-08 
  • Released Date: 2019-12-11 
  • Deposition Author(s): Shi, W., Gong, P.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2018YFA0507200
Ministry of Science and Technology (China)China2016YFC1200400
National Natural Science Foundation of ChinaChina31670154

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Database references