5MQX

NMR solution structure of macro domain from Venezuelan equine encephalitis virus(VEEV) in complex with ADP-ribose


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 112 
  • Conformers Submitted: 21 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational plasticity of the VEEV macro domain is important for binding of ADP-ribose.

Makrynitsa, G.I.Ntonti, D.Marousis, K.D.Birkou, M.Matsoukas, M.T.Asami, S.Bentrop, D.Papageorgiou, N.Canard, B.Coutard, B.Spyroulias, G.A.

(2019) J Struct Biol 206: 119-127

  • DOI: 10.1016/j.jsb.2019.02.008
  • Primary Citation of Related Structures:  
    5MQX, 5ISN

  • PubMed Abstract: 
  • Venezuelan equine encephalitis virus (VEEV) is a new world alphavirus which can be involved in several central nervous system disorders such as encephalitis and meningitis. The VEEV genome codes for 4 non-structural proteins (nsP), of which nsP3 contains a Macro domain ...

    Venezuelan equine encephalitis virus (VEEV) is a new world alphavirus which can be involved in several central nervous system disorders such as encephalitis and meningitis. The VEEV genome codes for 4 non-structural proteins (nsP), of which nsP3 contains a Macro domain. Macro domains (MD) can be found as stand-alone proteins or embedded within larger proteins in viruses, bacteria and eukaryotes. Their most common feature is the binding of ADP-ribose (ADPr), while several macro domains act as ribosylation writers, erasers or readers. Alphavirus MD erase ribosylation but their precise contribution in viral replication is still under investigation. NMR-driven titration experiments of ADPr in solution with the VEEV macro domain (in apo- and complex state) show that it adopts a suitable conformation for ADPr binding. Specific experiments indicate that the flexibility of the loops β5-α3 and α3-β6 is critical for formation of the complex and assists a wrapping mechanism for ADPr binding. Furthermore, along with this sequence of events, the VEEV MD undergoes a conformational exchange process between the apo state and a low-populated "dark" conformational state.


    Related Citations: 
    • NMR study of non-structural proteins--part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).
      Makrynitsa, G.I., Ntonti, D., Marousis, K.D., Tsika, A.C., Lichiere, J., Papageorgiou, N., Coutard, B., Bentrop, D., Spyroulias, G.A.
      (2015) Biomol NMR Assign 9: 247

    Organizational Affiliation

    Department of Pharmacy, University of Patras, GR-26504, Greece. Electronic address: G.A.Spyroulias@upatras.gr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein3A166Venezuelan equine encephalitis virus (strain P676)Mutation(s): 0 
Gene Names: NSP3
EC: 2.1.1 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1.3.33 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.1.3.84 (UniProt), 2.7.7.19 (UniProt)
Find proteins for P36328 (Venezuelan equine encephalitis virus (strain P676))
Explore P36328 
Go to UniProtKB:  P36328
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 112 
  • Conformers Submitted: 21 
  • Selection Criteria: target function 
  • OLDERADO: 5MQX Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
285950

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection