Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 45555.32 
• Atom Count: 3070 
• Residue Count: 399 
• Unique protein chains: 2

4RF0

Crystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease in complex with ubiquitin (space group P6522)

• DOI: 10.2210/pdb4RF0/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Human betacoronavirus 2c Jordan-N3/2012
• Expression System: Escherichia coli


• Deposited: 2014-09-24 Released: 2014-10-22 
• Deposition Author(s): Bailey-Elkin, B.A., Johnson, G.G., Mark, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.281 
• R-Value Work: 0.240 

Literature

Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression.

Bailey-Elkin, B.A., Knaap, R.C., Johnson, G.G., Dalebout, T.J., Ninaber, D.K., van Kasteren, P.B., Bredenbeek, P.J., Snijder, E.J., Kikkert, M., Mark, B.L.

(2014) J.Biol.Chem. 289: 34667-34682

• PubMed: 25320088 
• DOI: 10.1074/jbc.M114.609644
• Primary Citation of Related Structures:  
  4RF1, 4REZ


• PubMed Abstract: 
  

Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human pathogen that was first isolated in 2012. MERS-CoV replication depends in part on a virus-encoded papain-like protease (PL(pro)) that cleaves the viral replicase polyproteins at three sites releasing non-structural protein 1 (nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV PL(pro) was recently shown to be a deubiquitinating enzyme (DUB) and to possess deISGylating activity, as previously reported for other coronaviral PL(pro) domains, including that of severe acute respiratory syndrome coronavirus. These activities have been suggested to suppress host antiviral responses during infection. To understand the molecular basis for ubiquitin (Ub) recognition and deconjugation by MERS-CoV PL(pro), we determined its crystal structure in complex with Ub. Guided by this structure, mutations were introduced into PL(pro) to specifically disrupt Ub binding without affecting viral polyprotein cleavage, as determined using an in trans nsp3↓4 cleavage assay. Having developed a strategy to selectively disable PL(pro) DUB activity, we were able to specifically examine the effects of this activity on the innate immune response. Whereas the wild-type PL(pro) domain was found to suppress IFN-β promoter activation, PL(pro) variants specifically lacking DUB activity were no longer able to do so. These findings directly implicate the DUB function of PL(pro), and not its proteolytic activity per se, in the inhibition of IFN-β promoter activity. The ability to decouple the DUB activity of PL(pro) from its role in viral polyprotein processing now provides an approach to further dissect the role(s) of PL(pro) as a viral DUB during MERS-CoV infection.

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Organizational Affiliation: 

From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ORF1ab protein	A	324	Human betacoronavirus 2c Jordan-N3/2012	Mutation(s): 0  Gene Names: ORF1ab
Find proteins for M4STU1 (Human betacoronavirus 2c Jordan-N3/2012) Go to UniProtKB:  M4STU1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-60S ribosomal protein L40	B	75	Homo sapiens	Mutation(s): 0  Gene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens) Go to Gene View: UBA52 Go to UniProtKB:  P62987

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
3CN	B	3-AMINOPROPANE C3 H9 N WGYKZJWCGVVSQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.281 
• R-Value Work: 0.240 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 176.972	α = 90.00
b = 176.972	β = 90.00
c = 84.549	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
SCALA	data scaling
MxDC	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-24 
• Released Date: 2014-10-22 
• Deposition Author(s): Bailey-Elkin, B.A., Johnson, G.G., Mark, B.L.

Revision History 

• Version 1.0: 2014-10-22
  Type: Initial release
• Version 1.1: 2014-10-29
  Type: Database references
• Version 1.2: 2015-01-14
  Type: Database references