8OIV | pdb_00008oiv

Monkeypox virus VP39 in complex with SAH and cap0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.245 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural basis for RNA-cap recognition and methylation by the mpox methyltransferase VP39.

Skvara, P.Chalupska, D.Klima, M.Kozic, J.Silhan, J.Boura, E.

(2023) Antiviral Res 216: 105663-105663

  • DOI: https://doi.org/10.1016/j.antiviral.2023.105663
  • Primary Citation Related Structures: 
    8OIV

  • PubMed Abstract: 

    Mpox is a zoonotic disease caused by the mpox virus (MPXV), which has gained attention due to its rapid and widespread transmission, with reports from more than 100 countries. The virus belongs to the Orthopoxvirus genus, which also includes variola virus and vaccinia virus. In poxviruses, the RNA cap is crucial for the translation and stability of viral mRNAs and also for immune evasion. This study presents the crystal structure of the mpox 2'-O-methyltransfarase VP39 in complex with a short cap-0 RNA. The RNA substrate binds to the protein without causing any significant changes to its overall fold and is held in place by a combination of electrostatic interactions, π-π stacking and hydrogen bonding. The structure also explains the mpox VP39 preference for a guanine base at the first position; it reveals that guanine forms a hydrogen bond that an adenine would not be able to form.


  • Organizational Affiliation
    • Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, V.v.i, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 75.86 kDa 
  • Atom Count: 5,200 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 620 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
A, B
307Monkeypox virusMutation(s): 0 
Gene Names: 
EC: 2.1.1.57
UniProt
Find proteins for A0A7H0DN74 (Monkeypox virus)
Explore A0A7H0DN74 
Go to UniProtKB:  A0A7H0DN74
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7H0DN74
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
mGpppGAAAAAC [auth D]6synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.245 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.77α = 90
b = 84.89β = 90
c = 155.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionLX22NPO5103

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Structure summary