5DUS | pdb_00005dus

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

• PDB DOI: https://doi.org/10.2210/pdb5DUS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-20 Released: 2016-01-13 
• Deposition Author(s): Cho, C.-C., Lin, M.-H., Chuang, C.-Y., Hsu, C.-H.
• Funding Organization(s): the Ministry of Science and Technology, National Taiwan University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

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 Biological Chem 291: 4894-4902

• PubMed: 26740631 
• DOI: https://doi.org/10.1074/jbc.M115.700542
• Primary Citation 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 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.

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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.
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 [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.81 kDa 
• Atom Count: 1,492 
• Modeled Residue Count: 165 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1a	A	168	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N638  Go to UniProtKB:  K9N638

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	B [auth A]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.798	α = 90
b = 120.807	β = 90
c = 67.659	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Cho, C.-C., Lin, M.-H., Chuang, C.-Y., Hsu, C.-H.

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Funding Organization	Location	Grant Number
the Ministry of Science and Technology	Taiwan	103-2113-M-002-009-MY2
National Taiwan University	Taiwan	NTU-ERP-104R8600
National Taiwan University	Taiwan	NTU-ICRP-104R7560-5

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations