2PX8

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and 7M-GTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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Literature

Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues.

Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Bressanelli, S., Owens, R.J., Stuart, D.I., Grimes, J.M.

(2007) J Gen Virol 88: 2228-2236

  • DOI: https://doi.org/10.1099/vir.0.82757-0
  • Primary Citation of Related Structures:  
    2PX2, 2PX4, 2PX5, 2PX8, 2PXA, 2PXC

  • PubMed Abstract: 

    We have determined the high resolution crystal structure of the methyltransferase domain of the NS5 polypeptide from the Murray Valley encephalitis virus. This domain is unusual in having both the N7 and 2'-O methyltransferase activity required for Cap 1 synthesis. We have also determined structures for complexes of this domain with nucleotides and cap analogues providing information on cap binding, based on which we suggest a model of how the sequential methylation of the N7 and 2'-O groups of the cap may be coordinated.

    • Organizational Affiliation: 

    Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]
A, B
269Murray valley encephalitis virus (strain MVE-1-51)Mutation(s): 4 
Gene Names: NS5
EC: 2.7.7.48
UniProt
Find proteins for P05769 (Murray valley encephalitis virus (strain MVE-1-51))
Explore P05769 
Go to UniProtKB:  P05769
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05769
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B],
I [auth B]		7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
SAH
Query on SAH
Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]		S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
3PO
Query on 3PO
Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]		TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.579α = 90
b = 87.445β = 90
c = 100.914γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description