6R0F

Getah virus macro domain in complex with ADPr, pose 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/s41598-020-70870-w
  • Primary Citation of Related Structures:  
    6QZU, 6R0P, 6R0R, 6R0G, 6R0F, 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 ...

    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

    Unité des Virus Emergents (UVE), Aix Marseille Univ-IRD 190-INSERM 1207-IHU Méditerranée Infection, 13005, Marseille, France. bruno.coutard@univ-amu.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural polyproteinA, B168Getah virusMutation(s): 0 
Gene Names: nsP1234
EC: 2.1.1 (UniProt), 2.7.7 (UniProt), 3.1.3.33 (UniProt), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 3.1.3.84 (UniProt), 2.7.7.19 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q5Y389 (Getah virus)
Explore Q5Y389 
Go to UniProtKB:  Q5Y389
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
C [auth A], D [auth B][(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.729α = 90
b = 71.566β = 90
c = 98.693γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references