6JXM

Crystal Structure of phi29 pRNA domain II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.

Cai, R.Price, I.R.Ding, F.Wu, F.Chen, T.Zhang, Y.Liu, G.Jardine, P.J.Lu, C.Ke, A.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz692

  • PubMed Abstract: 
  • Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed ligh ...

    Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA-gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a 'Z'-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.,National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.,Department of Diagnostic and Biological Sciences, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.,Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (97-mer)B97Bacillus virus phi29
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.178α = 90.00
b = 120.178β = 90.00
c = 187.494γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31300603

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release