2JZE

NMR structure of the domain 527-651 of the SARS-CoV nonstructural protein nsp3, single conformer closest to the mean coordinates of an ensemble of twenty energy minimized conformers


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.

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

(2009) J Virol 83: 1823-1836

  • DOI: 10.1128/JVI.01781-08
  • Primary Citation of Related Structures:  
    2JZD, 2JZE, 2JZF, 2RNK

  • PubMed Abstract: 
  • The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined ...

    The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1"-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.


    Organizational Affiliation

    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase polyprotein 1abA129Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations