6KWR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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This is version 1.3 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.

(2020) Nucleic Acids Res 48: 1392-1405

  • DOI: https://doi.org/10.1093/nar/gkz1170
  • Primary Citation of Related Structures:  
    6KWQ, 6KWR

  • 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 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

    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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase468Enterovirus A71Mutation(s): 0 
Gene Names: CN12_49082gpPOL
EC: 2.7.7.48
UniProt
Find proteins for M4QLY4 (Human enterovirus 71)
Explore M4QLY4 
Go to UniProtKB:  M4QLY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4QLY4
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (31-MER)31synthetic construct
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))-3')13synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.008α = 90
b = 76.454β = 94.92
c = 68.075γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description