2PX2

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 1)

• PDB DOI: https://doi.org/10.2210/pdb2PX2/pdb

• Classification: TRANSFERASE
• Organism(s): Murray valley encephalitis virus (strain MVE-1-51)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-14 Released: 2007-05-29 
• Deposition Author(s): Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Owens, R.J., Stuart, D.I., Grimes, J.M., Oxford Protein Production Facility (OPPF)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 

Starting Model: experimental

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

• PubMed: 17622627 
• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.63 kDa 
• Atom Count: 4,409 
• Modelled Residue Count: 506 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	269	Murray valley encephalitis virus (strain MVE-1-51)	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	F [auth A], K [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.4	α = 90
b = 68.3	β = 98.4
c = 82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Assenberg, R., Ren, J., Verma, A., Walter, T.S., Alderton, D., Hurrelbrink, R.J., Fuller, S.D., Owens, R.J., Stuart, D.I., Grimes, J.M., Oxford Protein Production Facility (OPPF)

Revision History  

• 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: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description