6JYT

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis.

Jia, Z., Yan, L., Ren, Z., Wu, L., Wang, J., Guo, J., Zheng, L., Ming, Z., Zhang, L., Lou, Z., Rao, Z.

(2019) Nucleic Acids Res 47: 6538-6550

  • DOI: 10.1093/nar/gkz409
  • Primary Citation of Related Structures:  
    6JYT

  • PubMed Abstract: 

    • To date, an effective therapeutic treatment that confers strong attenuation toward coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs is considered to be one of the most important. Here, we first present the structure of the full-length Nsp13 helicase of SARS-CoV (SARS-Nsp13) and investigate the structural coordination of its five domains and how these contribute to its translocation and unwinding activity ...

    To date, an effective therapeutic treatment that confers strong attenuation toward coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs is considered to be one of the most important. Here, we first present the structure of the full-length Nsp13 helicase of SARS-CoV (SARS-Nsp13) and investigate the structural coordination of its five domains and how these contribute to its translocation and unwinding activity. A translocation model is proposed for the Upf1-like helicase members according to three different structural conditions in solution characterized through H/D exchange assay, including substrate state (SARS-Nsp13-dsDNA bound with AMPPNP), transition state (bound with ADP-AlF4-) and product state (bound with ADP). We observed that the β19-β20 loop on the 1A domain is involved in unwinding process directly. Furthermore, we have shown that the RNA dependent RNA polymerase (RdRp), SARS-Nsp12, can enhance the helicase activity of SARS-Nsp13 through interacting with it directly. The interacting regions were identified and can be considered common across CoVs, which provides new insights into the Replication and Transcription Complex (RTC) of CoVs.

    Organizational Affiliation: 

    Shanghai Institute for Advanced Immunochemical Studies and iHuman Institute, ShanghaiTech University, Shanghai 201210, China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HelicaseA, B603Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep, 1a-1b
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (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
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.99α = 90
b = 189.15β = 102.89
c = 57.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-28 
  • Released Date: 2019-09-18 
    • Deposition Author(s): Yan, L., Jia, Z.
Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFC0840302

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release