5F8J

Enterovirus 71 Polymerase Elongation Complex (C1S4 Form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.675 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation

Shu, B.Gong, P.

(2016) Proc.Natl.Acad.Sci.USA 113: E4005-E4014

  • DOI: 10.1073/pnas.1602591113
  • Primary Citation of Related Structures:  5F8G, 5F8H, 5F8I, 5F8L, 5F8M, 5F8N

  • PubMed Abstract: 
  • Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain ...

    Viral RNA-dependent RNA polymerases (RdRPs) play essential roles in viral genome replication and transcription. We previously reported several structural states of the poliovirus RdRP nucleotide addition cycle (NAC) that revealed a unique palm domain-based active site closure mechanism and proposed a six-state NAC model including a hypothetical state representing translocation intermediates. Using the RdRP from another human enterovirus, enterovirus 71, here we report seven RdRP elongation complex structures derived from a crystal lattice that allows three NAC events. These structures suggested a key order of events in initial NTP binding and NTP-induced active site closure and revealed a bona fide translocation intermediate featuring asymmetric movement of the template-product duplex. Our work provides essential missing links in understanding NTP recognition and translocation mechanisms in viral RdRPs and emphasizes the uniqueness of the viral RdRPs compared with other processive polymerases.


    Organizational Affiliation

    Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, 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
Genome polyprotein
A
468Enterovirus A71N/A
Find proteins for E5RPG2 (Enterovirus A71)
Go to UniProtKB:  E5RPG2
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (35-MER)B35synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*C)-3')C17synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.675 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.430α = 90.00
b = 76.572β = 90.00
c = 149.267γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-09 
  • Released Date: 2016-06-22 
  • Deposition Author(s): Shu, B., Gong, P.

Funding OrganizationCountryGrant Number
Ministry of Science and TechnologyChina2013CB9111

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references