2XBM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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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: https://doi.org/10.1371/journal.pone.0012836
  • Primary Citation of Related Structures:  
    2XBM

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NONSTRUCTURAL PROTEIN NS5
A, B, C, D
263Dengue virusMutation(s): 0 
UniProt
Find proteins for C0LMU5 (dengue virus type 3)
Explore C0LMU5 
Go to UniProtKB:  C0LMU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0LMU5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
E, F
9N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth B],
U [auth C],
X [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4
Query on SO4

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.543α = 90
b = 137.543β = 90
c = 109.385γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description