3GZF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.756 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.240 

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.,Sect.D 65: 839-846

  • DOI: 10.1107/S0907444909018253

  • 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 polypro ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1ab
A, B, C, D, E
96Feline coronavirus (strain FIPV WSU-79/1146)Mutation(s): 0 
Gene Names: rep
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Go to UniProtKB:  Q98VG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.756 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.240 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 127.538α = 90.00
b = 127.538β = 90.00
c = 42.797γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
BP3phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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