3GZF

Structure of the C-terminal domain of nsp4 from Feline Coronavirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the C-terminal domain of nsp4 from feline coronavirus

Manolaridis, I.Wojdyla, J.A.Panjikar, S.Snijder, E.J.Gorbalenya, A.E.Berglind, H.Nordlund, P.Coutard, B.Tucker, P.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 839-846

  • DOI: 10.1107/S0907444909018253
  • Primary Citation of Related Structures:  
    3GZF

  • PubMed Abstract: 
  • Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26-31 kb) encodes 15-16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing ...

    Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26-31 kb) encodes 15-16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication-transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain ( approximately 100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8 A resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P4(3). The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly alpha-helical content displaying a unique fold that could be engaged in protein-protein interactions.


    Organizational Affiliation

    EMBL Hamburg Outstation, D-22603 Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase polyprotein 1abA, B, C, D, E96Feline coronavirusMutation(s): 0 
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Explore Q98VG9 
Go to UniProtKB:  Q98VG9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth C], G [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.538α = 90
b = 127.538β = 90
c = 42.797γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BP3phasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance