6JYT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 

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

  • 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 ...

    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

    State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin 300353, China.,State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,Protein Chemistry Facility, Center for Biomedical Analysis of Tsinghua University, Beijing 100084, China.,State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China.,Shanghai Institute for Advanced Immunochemical Studies and iHuman Institute, ShanghaiTech University, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Helicase
A, B
603Human SARS coronavirusMutation(s): 0 
Gene Names: rep
Find proteins for P0C6X7 (Human SARS coronavirus)
Go to UniProtKB:  P0C6X7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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: 2.8 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 191.990α = 90.00
b = 189.150β = 102.89
c = 57.330γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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