3UB0 | pdb_00003ub0

Crystal structure of the nonstructural protein 7 and 8 complex of Feline Coronavirus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.227 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity.

Xiao, Y.Ma, Q.Restle, T.Shang, W.Svergun, D.I.Ponnusamy, R.Sczakiel, G.Hilgenfeld, R.

(2012) J Virol 86: 4444-4454

  • DOI: https://doi.org/10.1128/JVI.06635-11
  • Primary Citation Related Structures: 
    3UB0

  • PubMed Abstract: 

    Nonstructural proteins 7 and 8 of severe acute respiratory syndrome coronavirus (SARS-CoV) have previously been shown by X-ray crystallography to form an 8:8 hexadecamer. In addition, it has been demonstrated that N-terminally His(6)-tagged SARS-CoV Nsp8 is a primase able to synthesize RNA oligonucleotides with a length of up to 6 nucleotides. We present here the 2.6-Å crystal structure of the feline coronavirus (FCoV) Nsp7:Nsp8 complex, which is a 2:1 heterotrimer containing two copies of the α-helical Nsp7 with conformational differences between them, and one copy of Nsp8 that consists of an α/β domain and a long-α-helix domain. The same stoichiometry is found for the Nsp7:Nsp8 complex in solution, as demonstrated by chemical cross-linking, size exclusion chromatography, and small-angle X-ray scattering. Furthermore, we show that FCoV Nsp8, like its SARS-CoV counterpart, is able to synthesize short oligoribonucleotides of up to 6 nucleotides in length when carrying an N-terminal His(6) tag. Remarkably, the same protein harboring the sequence GPLG instead of the His(6) tag at its N terminus exhibits a substantially increased, primer-independent RNA polymerase activity. Upon addition of Nsp7, the RNA polymerase activity is further enhanced so that RNA up to template length (67 nucleotides) can be synthesized. Further, we show that the unprocessed intermediate polyprotein Nsp7-10 of human coronavirus (HCoV) 229E is also capable of synthesizing oligoribonucleotides up to a chain length of six. These results indicate that in case of FCoV as well as of HCoV 229E, the formation of a hexadecameric Nsp7:Nsp8 complex is not necessary for RNA polymerase activity. Further, the FCoV Nsp7:Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length.


  • Organizational Affiliation
    • Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany.

Macromolecule Content 

  • Total Structure Weight: 83.05 kDa 
  • Atom Count: 5,575 
  • Modeled Residue Count: 707 
  • Deposited Residue Count: 746 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 6, nsp6,
A, D
199Feline infectious peritonitis virus (strain 79-1146)Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Explore Q98VG9 
Go to UniProtKB:  Q98VG9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98VG9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 7, nsp7
B, C, E, F
87Feline infectious peritonitis virus (strain 79-1146)Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Explore Q98VG9 
Go to UniProtKB:  Q98VG9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98VG9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.227 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.454α = 90
b = 160.301β = 90
c = 102.66γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SHELXDphasing
SHELXEmodel building
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary