4YPT

X-ray structural of three tandemly linked domains of nsp3 from murine hepatitis virus at 2.60 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6009 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions.

Chen, Y.Savinov, S.N.Mielech, A.M.Cao, T.Baker, S.C.Mesecar, A.D.

(2015) J.Biol.Chem. 290: 25293-25306

  • DOI: 10.1074/jbc.M115.662130

  • PubMed Abstract: 
  • Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus ...

    Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional studies on MHV and its nsp3 domain, the structure of only one domain in nsp3, the small ubiquitin-like domain 1 (Ubl1), has been determined. We report here the x-ray structure of three tandemly linked domains of MHV nsp3, including the papain-like protease 2 (PLP2) catalytic domain, the ubiquitin-like domain 2 (Ubl2), and a third domain that we call the DPUP (domain preceding Ubl2 and PLP2) domain. DPUP has close structural similarity to the severe acute respiratory syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to the severe acute respiratory syndrome coronavirus. The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating isopeptidase activities in addition to proteolytic activity. A computationally derived model of MHV PLP2 bound to ubiquitin was generated, and the potential interactions between ubiquitin and PLP2 were probed by site-directed mutagenesis. These studies extend substantially our structural knowledge of MHV nsp3, providing a platform for further investigation of the role of nsp3 domains in MHV viral replication.


    Organizational Affiliation

    From the Department of Biological Sciences, the Center for Cancer Research, and the Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 and amesecar@purdue.edu.,the Center for Cancer Research, and.,the Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153.,From the Department of Biological Sciences.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1ab
A
387Murine coronavirus (strain A59)Mutation(s): 0 
Gene Names: rep
Find proteins for P0C6X9 (Murine coronavirus (strain A59))
Go to UniProtKB:  P0C6X9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6009 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 155.576α = 90.00
b = 155.576β = 90.00
c = 155.576γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI085089

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Other, Structure summary
  • Version 1.2: 2015-09-09
    Type: Database references
  • Version 1.3: 2015-10-28
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.5: 2019-12-11
    Type: Author supporting evidence