2K87

NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS CORONAVIRUS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3.

Serrano, P.Johnson, M.A.Chatterjee, A.Neuman, B.W.Joseph, J.S.Buchmeier, M.J.Kuhn, P.Wuthrich, K.

(2009) J Virol 83: 12998-13008

  • DOI: https://doi.org/10.1128/JVI.01253-09
  • Primary Citation of Related Structures:  
    2K87

  • PubMed Abstract: 

    The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. Two antiparallel two-strand beta-sheets and two 3(10)-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.


  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., MB-44, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3 of Replicase polyprotein 1a116Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6U8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2023-02-01
    Changes: Database references
  • Version 1.4: 2023-06-14
    Changes: Other
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references