6R0R

Getah virus macro domain in complex with ADPr covalently bond to Cys34

• PDB DOI: https://doi.org/10.2210/pdb6R0R/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Getah virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-13 Released: 2020-04-01 
• Deposition Author(s): Ferreira Ramos, A.S., Sulzenbacher, G., Coutard, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.197 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Snapshots of ADP-ribose bound to Getah virus macro domain reveal an intriguing choreography.

Ferreira-Ramos, A.S., Sulzenbacher, G., Canard, B., Coutard, B.

(2020) Sci Rep 10: 14422-14422

• PubMed: 32879358 
• DOI: https://doi.org/10.1038/s41598-020-70870-w
• Primary Citation of Related Structures:  
  6QZU, 6R0F, 6R0G, 6R0P, 6R0R, 6R0T


• PubMed Abstract: 
  

  Alphaviruses are (re-)emerging arboviruses of public health concern. The nsP3 gene product is one of the key players during viral replication. NsP3 comprises three domains: a macro domain, a zinc-binding domain and a hypervariable region. The macro domain is essential at both early and late stages of the replication cycle through ADP-ribose (ADPr) binding and de-ADP-ribosylation of host proteins. However, both its specific role and the precise molecular mechanism of de-ADP-ribosylation across specific viral families remains to be elucidated. Here we investigate by X-ray crystallography the mechanism of ADPr reactivity in the active site of Getah virus macro domain, which displays a peculiar substitution of one of the conserved residues in the catalytic loop. ADPr adopts distinct poses including a covalent bond between the C''1 of the ADPr and a conserved Togaviridae-specific cysteine. These different poses observed for ADPr may represent snapshots of the de-ADP-ribosylation mechanism, highlighting residues to be further characterised.

---

Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 18.74 kDa 
• Atom Count: 1,442 
• Modelled Residue Count: 162 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural polyprotein	A	168	Getah virus	Mutation(s): 0  Gene Names: nsP1234
UniProt
Find proteins for Q5Y389 (Getah virus) Explore Q5Y389  Go to UniProtKB:  Q5Y389

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JNT	B [auth A]	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate C15 H25 N5 O14 P2 QKJRZYRQRSLXSV-AOOZFPJJSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.197 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.011	α = 90
b = 46.801	β = 104.16
c = 51.004	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Ferreira Ramos, A.S., Sulzenbacher, G., Coutard, B.

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary