5DUS

Crystal structure of MERS-CoV macro domain in complex with ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Macro Domain from Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Is an Efficient ADP-ribose Binding Module: CRYSTAL STRUCTURE AND BIOCHEMICAL STUDIES

Cho, C.-C.Lin, M.-H.Chuang, C.-Y.Hsu, C.-H.

(2016) J Biol Chem 291: 4894-4902

  • DOI: 10.1074/jbc.M115.700542
  • Primary Citation of Related Structures:  
    5DUS

  • PubMed Abstract: 
  • The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) encodes the conserved macro domain within non-structural protein 3. However, the precise biochemical function and structure of the macro domain is unclear. Using differential ...

    The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) encodes the conserved macro domain within non-structural protein 3. However, the precise biochemical function and structure of the macro domain is unclear. Using differential scanning fluorimetry and isothermal titration calorimetry, we characterized the MERS-CoV macro domain as a more efficient adenosine diphosphate (ADP)-ribose binding module than macro domains from other CoVs. Furthermore, the crystal structure of the MERS-CoV macro domain was determined at 1.43-Å resolution in complex with ADP-ribose. Comparison of macro domains from MERS-CoV and other human CoVs revealed structural differences in the α1 helix alters how the conserved Asp-20 interacts with ADP-ribose and may explain the efficient binding of the MERS-CoV macro domain to ADP-ribose. This study provides structural and biophysical bases to further evaluate the role of the MERS-CoV macro domain in the host response via ADP-ribose binding but also as a potential target for drug design.


    Organizational Affiliation

    From the Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, the Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, and the Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan andyhsu@ntu.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF1aA168Middle East respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt)
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N638 
Go to UniProtKB:  K9N638
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
APRKd:  3120   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.130 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.798α = 90
b = 120.807β = 90
c = 67.659γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Science and TechnologyTaiwan103-2113-M-002-009-MY2
National Taiwan UniversityTaiwanNTU-ERP-104R8600
National Taiwan UniversityTaiwanNTU-ICRP-104R7560-5

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references