2XBM

Crystal structure of the dengue virus methyltransferase bound to a 5'- capped octameric RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5'-Capped Octameric RNA

Yap, L.J.Luo, D.H.Chung, K.Y.Lim, S.P.Bodenreider, C.Noble, C.Shi, P.Y.Lescar, J.

(2010) Plos One 5: 12836

  • DOI: 10.1371/journal.pone.0012836

  • PubMed Abstract: 
  • The N-terminal domain of the flavivirus NS5 protein functions as a methyltransferase (MTase). It sequentially methylates the N7 and 2'-O positions of the viral RNA cap structure (GpppA→(7me)GpppA→(7me)GpppA(2'-O-me)). The same NS5 domain could also h ...

    The N-terminal domain of the flavivirus NS5 protein functions as a methyltransferase (MTase). It sequentially methylates the N7 and 2'-O positions of the viral RNA cap structure (GpppA→(7me)GpppA→(7me)GpppA(2'-O-me)). The same NS5 domain could also have a guanylyltransferase activity (GTP+ppA-RNA→GpppA). The mechanism by which this protein domain catalyzes these three distinct functions is currently unknown. Here we report the crystallographic structure of DENV-3 MTase in complex with a 5'-capped RNA octamer (G(ppp)AGAACCUG) at a resolution of 2.9 A. Two RNA octamers arranged as kissing loops are encircled by four MTase monomers around a 2-fold non-crystallography symmetry axis. Only two of the four monomers make direct contact with the 5' end of RNA. The RNA structure is stabilised by the formation of several intra and intermolecular base stacking and non-canonical base pairs. The structure may represent the product of guanylylation of the viral genome prior to the subsequent methylation events that require repositioning of the RNA substrate to reach to the methyl-donor sites. The crystal structure provides a structural explanation for the observed trans-complementation of MTases with different methylation defects.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NONSTRUCTURAL PROTEIN NS5
A, B, C, D
263Dengue virus 3Mutation(s): 0 
Find proteins for C0LMU5 (Dengue virus 3)
Go to UniProtKB:  C0LMU5
Entity ID: 2
MoleculeChainsLengthOrganism
5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'E,F9N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
G3A
Query on G3A
E, F
NON-POLYMERC20 H27 N10 O17 P3G,A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 137.543α = 90.00
b = 137.543β = 90.00
c = 109.385γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references, Non-polymer description, Version format compliance