2J98

Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Variable Oligomerization Modes in Coronavirus Non-Structural Protein 9.

Ponnusamy, R.Moll, R.Weimar, T.Mesters, J.R.Hilgenfeld, R.

(2008) J Mol Biol 383: 1081

  • DOI: https://doi.org/10.1016/j.jmb.2008.07.071
  • Primary Citation of Related Structures:  
    2J97, 2J98

  • PubMed Abstract: 

    Non-structural protein 9 (Nsp9) of coronaviruses is believed to bind single-stranded RNA in the viral replication complex. The crystal structure of Nsp9 of human coronavirus (HCoV) 229E reveals a novel disulfide-linked homodimer, which is very different from the previously reported Nsp9 dimer of SARS coronavirus. In contrast, the structure of the Cys69Ala mutant of HCoV-229E Nsp9 shows the same dimer organization as the SARS-CoV protein. In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Chemical cross-linking suggests similar modes of aggregation in solution. In zone-interference gel electrophoresis assays and surface plasmon resonance experiments, the HCoV-229E wild-type protein is found to bind oligonucleotides with relatively high affinity, whereas binding by the Cys69Ala and Cys69Ser mutants is observed only for the longest oligonucleotides. The corresponding mutations in SARS-CoV Nsp9 do not hamper nucleic acid binding. From the crystal structures, a model for single-stranded RNA binding by Nsp9 is deduced. We propose that both forms of the Nsp9 dimer are biologically relevant; the occurrence of the disulfide-bonded form may be correlated with oxidative stress induced in the host cell by the viral infection.


  • Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
REPLICASE POLYPROTEIN 1AB109Human coronavirus 229EMutation(s): 1 
UniProt
Find proteins for P0C6X1 (Human coronavirus 229E)
Explore P0C6X1 
Go to UniProtKB:  P0C6X1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
REPLICASE POLYPROTEIN 1AB109Human coronavirus 229EMutation(s): 1 
UniProt
Find proteins for P0C6X1 (Human coronavirus 229E)
Explore P0C6X1 
Go to UniProtKB:  P0C6X1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download Ideal Coordinates CCD File 
C [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.396α = 90
b = 61.377β = 90
c = 107.309γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description