Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.21 kDa 
• Atom Count: 539 
• Modelled Residue Count: 67 
• Deposited Residue Count: 198 
• Unique protein chains: 1

2KQW

SARS coronavirus-unique domain (SUD): Three-domain molecular architecture in solution and RNA binding. II: Structure of the SUD-C domain of SUD-MC

• PDB DOI: 10.2210/pdb2KQW/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-19 Released: 2010-02-02 
• Deposition Author(s): Johnson, M.A., Chatterjee, A., Wuthrich, K., Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding.

Johnson, M.A., Chatterjee, A., Neuman, B.W., Wuthrich, K.

(2010) J Mol Biol 400: 724-742

• PubMed: 20493876 
• DOI: 10.1016/j.jmb.2010.05.027
• Primary Citation of Related Structures:  
  2KAF, 2KQV, 2KQW


• PubMed Abstract: 
  

Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	198	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: 1a EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt)
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus) Explore P0C6U8  Go to UniProtKB:  P0C6U8

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2KQW Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-19 
• Released Date: 2010-02-02 
Deposition Author(s): Johnson, M.A., Chatterjee, A., Wuthrich, K., Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-15
  Changes: Database references, Derived calculations